BCR-ABL truncation mutations

ABSTRACT

Truncation variants of BCR-ABL mRNA that produces BCR-ABL proteins with a truncated C-terminus and its role in resistance to treatment with kinase inhibitors is described. Vectors for expressing the truncated gene products are described as well as recombinant cells that express the truncated gene products from cDNA constructs. Also provided are methods compositions and kits for detecting the BCR-ABL truncation variants. Also provided are methods for determining the prognosis of a patient diagnosed as having myeloproliferative disease, and methods for predicting the likelihood for resistance to a treatment with tyrosine kinase inhibitor in a patient diagnosed as having myeloproliferative disease. Additionally, methods for screening BCR-ABL tyrosine kinase domain inhibitors which rely on the recombinant cells are also disclosed.

CROSS-REFERENCE TO RELATED APPLICATION

This application is a continuation of U.S. patent application Ser. No.15/342,321, filed Nov. 3, 2016, which is a continuation of U.S. patentapplication Ser. No. 12/892,679, filed Sep. 28, 2010, now U.S. Pat. No.9,488,656, which claims the benefit of U.S. Provisional Application61/247,390 filed on Sep. 30, 2009 both of which are hereby incorporatedby reference in their entirety.

The instant application contains a Sequence Listing which has beensubmitted in ASCII format via EFS-WEB and is hereby incorporated byreference in its entirety. Said ASCII copy, created on Sep. 27, 2018, isnamed sequence.txt and is 80 KB.

FIELD OF THE INVENTION

The present inventions relate to BCR-ABL variants and resistance tokinase inhibitor therapy.

BACKGROUND OF THE INVENTION

The following description is provided to assist the understanding of thereader. None of the information provided or references cited is admittedto be prior art to the present invention.

Myeloproliferative diseases such as Chronic Myelogenous Leukemia (CML),Acute Myelogenous Leukemia (AML) and Acute Lymphoblastic Leukemia (ALL)are associated with a specific chromosomal abnormality calledPhiladelphia chromosome. The genetic defect is caused by the reciprocaltranslocation designated t(9;22)(q34;q11), which refers to an exchangeof genetic material between region q34 of chromosome 9 and region q11 ofchromosome 22 (Rowley, J. D. Nature. 1973; 243: 290-3; Kurzrock et al.N. Engl. J. Med. 1988; 319: 990-998). This translocation results in aportion of the BCR (“breakpoint cluster region”) gene from chromosome 22(region q11) becoming fused with a portion of the ABL gene fromchromosome 9 (region q34).

The fused “BCR-ABL” gene is located on chromosome 22, in which both BCRand ABL genes are shortened as a result of the translocation. The fusedgene retains the tyrosine kinase domain of the ABL gene, which isconstitutively active (Elefanty et al. EMBO J. 1990; 9: 1069-1078). Thiskinase activity activates various signal transduction pathways leadingto uncontrolled cell growth and division (e.g., by promoting cellproliferation and inhibiting apoptosis). For example, BCR-ABL may causeundifferentiated blood cells to proliferate and fail to mature.

Treatment of myeloproliferative diseases may involve drug therapy (e.g.,chemotherapy), bone marrow transplants, or a combination. Protein kinaseinhibitors such as “imatinib mesylate” (also known as STI571 or2-phenylaminopyrimidine or “imantinib” for short; marketed as a drugunder the trade name “Gleevec” or “Glivec”) have proven effective fortreating CML (Deininger et al., Blood. 1997; 90: 3691-3698; Manley, P.W., Eur. J. Cancer. 2002; 38: S19-S27). Imatinib is an ATP competitiveinhibitor of TYROSINE KINASE activity and functions by binding to thekinase domain of BCR-ABL and stabilizing the protein in its closed,inactive conformation. Monotherapy with imatinib has been shown to beeffective for all stages of CML. Other kinase inhibitor drugs fortreating myeloproliferative diseases include Nilotinib, Dasatinib,Bosutinib (SKI-606) and Aurora kinase inhibitor VX-680.

Resistance to imatinib remains a major problem in the management ofpatients with myeloproliferative diseases. Rates at which primary (e.g.,failure to achieve any hematologic response) and secondary resistance(e.g., hematologic recurrence) occurs varies with the stage of diseases.Primary resistance has been reported in chronic-, accelerated-, orblast-phase at rates of 3%, 9%, and 51%, respectively (Melo, J. V. &Chuah, C. Cancer Lett. 2007; 249: 121-132; Hughes, T. Blood. 2006; 108:28-37). Secondary resistance has been reported in these patients atrates of 22%, 32%, and 41%, respectively.

Mutations that result in kinase inhibitor resistance include mutationsin the kinase domain of the BCR-ABL protein (Mahon, F. X. Blood. 2000;96: 1070-1079); mutations that disrupt critical contact points betweenimatinib and the tyrosine kinase receptor or induce a transition fromthe inactive to the active protein configuration, preventing imatinibbinding (Nagar, B. Cell. 2003; 112: 859-871; Nagar et al., Cancer Res.2002; 62: 4236-4243; Branford S. Blood. 2002; 99: 3472-3475; Branford etal. Blood. 2003; 102: 276-283); the T315I mutation (Gorre et al.Science. 2001; 293: 876-880; Hochhaus et al. Leukemia. 2002; 16:2190-2196); and P-loop mutations of BCR-ABL (Branford et al. Blood.2002; 99: 3472-3475; Branford et al. Blood. 2003; 102: 276-283; andGorre et al. Blood. 2002; 100: 3041-3044) The role of Src family kinasesare another possible mechanism for imatinib resistance (Levinson et al.,PLoS Biol. 2006; 4: e144). Overexpression and activation of LYN kinasehas been implicated in imatinib-resistance (Donato, N. J. Blood. 2003;101: 690-698).

Chu et al. (N. Engl. J. Med. 2006; 355: 10) report a truncation mutantof BCR-ABL in a CIVIL patient resistant to imatinib. Chu et al. reportthat the mutant results from a 35 base insertion of ABL intron 8 intothe junction between exons 8 and 9, resulting in a new C-terminus andtruncation of the normal C-terminus of the ABL portion of the fusionprotein. Laudadio et al. (J. Mol. Diag. 2008; 10(2): 177-180) alsoreports a similar splice variant in CML patients that had undergoneimatinib therapy. Guerrasio, et al. (Leukemia Research. 2008; 32:505-520) report a truncation mutant in patients with imatinib resistancehaving an alternatively spliced transcript lacking exon 7.

SUMMARY OF THE INVENTION

Provided herein are compositions and methods based on BCR-ABL nucleicacid variants that result in truncation of the BCR-ABL protein and thefinding that the BCR-ABL protein variants provide resistance to kinasedomain inhibitors such as imatinib. Provided are 4 novel mutations inBCR-ABL nucleic acid: a deletion of nucleotides 2595-2779 (Del2595-2779), insertion of tetranucleotides CAGG immediately afternucleotide position of 2417 (2417insCAGG), deletion of GA at nucleotideposition 2596-2597 (Del 2596-2597), and a substitution of C to T atposition 2506(C2506T) corresponding to SEQ ID NO: 1.

An isolated polynucleotide encoding at least a portion of the BCR-ABLnucleic acid in which the polynucleotide encodes the Del 2595-2779mutation is provided. In one example, the polynucleotide includes asequence that is substantially identical to SEQ ID NO: 4 over a stretchof 25 contiguous nucleotides. In one example, the sequence of isolatedpolynucleotide is SEQ ID NO: 3.

The Del 2595-2779 mutation results in a premature “TGA” stop codon atposition 2836-2838 of SEQ ID NO: 3. This mutation results in a truncatedBCR-ABL protein having new amino acids at the C-terminus. In oneexample, at least a portion of the truncated BCR-ABL protein issubstantially identical to SEQ ID NO: 6 over a stretch of 15 contiguousamino acids. In one example, the truncated protein has the amino acidsequence of SEQ ID NO: 6. In one example, the new C-terminal sequence isSEQ ID NO: 20. In one example, the amino acid sequence of the truncatedprotein is SEQ ID NO: 5.

An isolated polynucleotide encoding at least a portion of the BCR-ABLnucleic acid in which the polynucleotide encodes the Del 2596-2597mutation is also provided. In one example, the polynucleotide includes asequence that is substantially identical to SEQ ID NO: 8 over a stretchof 20 contiguous nucleotides. In one example, the sequence of isolatedpolynucleotide is SEQ ID NO: 7.

The Del 2596-2597 mutation results in a premature “TGA” stop codon atposition 2647-2649 of SEQ ID NO: 7. This mutation results in a truncatedBCR-ABL protein having new amino acids at the C-terminus. In oneexample, at least a portion of the truncated BCR-ABL protein issubstantially identical to SEQ ID NO: 10 over a stretch of 20 contiguousamino acids. In one example, the truncated protein has the amino acidsequence of SEQ ID NO: 9. In one example, the new C-terminal sequence isSEQ ID NO: 11.

An isolated polynucleotide encoding at least a portion of the BCR-ABLnucleic acid in which the polynucleotide encodes the 2417insCAGGmutation is also provided. In one example, the polynucleotide includes asequence that is substantially identical to SEQ ID NO: 13 over a stretchof 20 contiguous nucleotides. In one example, the sequence of isolatedpolynucleotide is SEQ ID NO: 12.

The 2417insCAGG mutation results in a premature “TGA” stop codon atposition 2647-2649 of SEQ ID NO: 12. This mutation results in atruncated BCR-ABL protein having new amino acids at the C-terminus. Inone example, at least a portion of the truncated BCR-ABL protein issubstantially identical to SEQ ID NO: 15 over a stretch of 20 contiguousamino acids. In one example, the truncated protein has the amino acidsequence of SEQ ID NO: 14. In one example, the new C-terminal amino acidsequence is SEQ ID NO: 16.

An isolated polynucleotide encoding at least a portion of the BCR-ABLnucleic acid in which the polynucleotide encodes the C2506T mutation isalso provided. In one example, the polynucleotide includes a sequencethat is substantially identical to SEQ ID NO: 18 over a stretch of 20contiguous nucleotides. In one example, the sequence of isolatedpolynucleotide is SEQ ID NO: 17.

The C2506T mutation results in a premature “TAG” stop codon at position2506-2508 of SEQ ID NO: 17. This mutation results in a truncated BCR-ABLprotein having new amino acids at the C-terminus. In one example, atleast a portion of the truncated BCR-ABL protein is substantiallyidentical to SEQ ID NO: 19. In one example, the truncated protein hasthe amino acid sequence of SEQ ID NO: 19.

Also provided are methods for detecting the presence or absence of amutation in BCR-ABL nucleic acid in an individual. The method includesa) providing a sample comprising BCR-ABL nucleic acid from theindividual and b) detecting the presence or absence of BCR-ABL nucleicacid comprising all or portions of nucleic acid selected from the groupconsisting of SEQ ID NO: 4, SEQ ID NO: 8, SEQ ID NO: 13, and SEQ ID NO:18; in which the presence of a nucleic acid comprising at least one ofSEQ ID NO: 4, SEQ ID NO: 8, SEQ ID NO: 13, and SEQ ID NO: 18 isindicative of the presence of at least one of mutations Del 2595-2779,Del 2596-2597, 2417insCAGG and C2506T in BCR-ABL nucleic acid. In oneexample, detecting the presence of SEQ ID NO: 4 is indicative of themutation Del 2595-2779 in BCR-ABL nucleic acid. In one example,detecting the presence of SEQ ID NO: 8 is indicative of the mutation Del2596-2597 in BCR-ABL nucleic acid. In another example, detecting thepresence of SEQ ID NO: 13 is indicative of the mutation 2417insCAGG inBCR-ABL nucleic acid. In another example, detecting the presence of SEQID NO: 18 is indicative of the mutation C2506T in BCR-ABL nucleic acid.In one example, the method includes sequencing BCR-ABL nucleic acid. Inanother example, the method includes assessing the size of said BCR-ABLnucleic acid. In one example, the BCR-ABL truncation mutations encodeamino acid sequences comprising one or more amino acid sequencesselected from the group consisting of SEQ ID NO: 6, SEQ ID NO: 10, SEQID NO: 15, and SEQ ID NO: 19.

Also provided are methods for predicting the likelihood for resistanceto treatment with a tyrosine kinase inhibitor in a patient diagnosed ashaving a myeloproliferative disease. In one example, the method includesassessing the BCR-ABL nucleic acid of the patient for the presence orabsence of one or more BCR-ABL mutations selected from the groupconsisting of Del 2595-2779, Del 2596-2597, 2417insCAGG, and C2506T;identifying the patient as having a likelihood of resistance to atyrosine kinase inhibitor when one or more of the mutations are present.In another example, the method includes assessing a sample from thepatient for the presence or absence of one or more BCR-ABL truncationmutant proteins encoded by BCR-ABL nucleic acid having one or moremutations selected from the group consisting of Del 2595-2779,2417insCAGG, Del 2596-2597, and C2506T; b) identifying the patient ashaving a likelihood of resistance to a tyrosine kinase inhibitor whenone or more of the truncation mutant proteins are present. In oneexample, the patient is administered with tyrosine kinase inhibitors.Exemplary tyrosine kinase inhibitors include but are not limited toimatinib, nilotinib, and dasatinib. In one example, the treatmentregiment of the patient is modified when at least one of the mutationsis identified.

Also provided are methods for determining the prognosis of a patientdiagnosed as having a myeloproliferative disease. In one example, themethod includes a) assessing the BCR-ABL nucleic acid of the patient forthe presence or absence of one or more BCR-ABL truncation mutationsselected from the group consisting of Del 2595-2779, 2417insCAGG, Del2596-2597, and C2506T, b) identifying the patient as having poorprognosis when one or more such mutations are present in BCR-ABL nucleicacid relative to an individual without one or more of such mutations inBCR-ABL nucleic acid. In another example, the method includes assessinga sample from the patient for the presence or absence of one or moreBCR-ABL truncation mutant proteins encoded by BCR-ABL nucleic acidhaving one or more mutations selected from the group consisting of Del2595-2779, 2417insCAGG, Del 2596-2597, and C2506T; b) identifying thepatient as having poor prognosis when one or more BCR-ABL truncationmutant proteins are present in the patient's sample relative to anindividual without such BCR-ABL truncation mutant proteins.

Also provided are methods for altering the treatment of a patientdiagnosed as having a myeloproliferative disease undergoing kinaseinhibitor therapy. In one example, the method includes a) assessing theBCR-ABL nucleic acid of the patient for the presence or absence of oneor more BCR-ABL truncation mutations selected from the group consistingof Del 2595-2779, 2417insCAGG, Del 2596-2597, and C2506T, b) identifyingthe patient as resistant to kinase inhibitors when one or more mutationsare present, c) altering the treatment of the patient by substitutingkinase inhibitors with alternative treatment. In another example, themethod includes assessing a sample from the patient for the presence orabsence of one or more BCR-ABL truncation mutant proteins encoded byBCR-ABL nucleic acid having one or more mutations in which one or moremutations is selected from the group consisting of Del 2595-2779, Del2596-2597, 2417insCAGG, C2506T, b) identifying the patient as resistantto kinase inhibitors when one or more of such truncation mutant proteinsare present, c) altering the treatment of the patient by substitutingkinase inhibitors with alternative treatment. Exemplary alternativetreatments include but are not limited to different tyrosine kinaseinhibitor, different inhibitor for BCR-ABL (e.g., antibodies specificfor BCR-ABL protein), and bone marrow transplant.

In some examples of the above aspects of the invention, themyeloproliferative disease is chronic myelogenous leukemia (CML) oracute lymphoblastic leukemia (ALL). In one example of the above aspectsof the invention, the myeloproliferative disease is CIVIL. In anotherexample of the above aspects of the invention, the myeloproliferativedisease is ALL. In one example of the above aspects of the invention,the mutation in BCR-ABL nucleic acid is Del 2595-2779. In anotherexample of the above aspects of the invention, the mutation in BCR-ABLnucleic acid is Del 2596-2597. In another example of the above aspectsof the invention, the mutation in BCR-ABL nucleic acid is 2417insCAGG.In another example of the above aspects of the invention, the mutationin BCR-ABL nucleic acid is C2506T. In some example s of the aboveaspects of the invention, the tyrosine kinase inhibitor used in thetreatment of a patient diagnosed as having a myeloproliferative diseaseis one or more selected from the group consisting of imatinib, nilotiniband dasatinib. In one example of the above aspects of the invention, thetyrosine kinase inhibitor is imatinib.

Also provided herein are antibodies that specifically bind to an epitopecomprising the new C-terminus of the truncated BCR-ABL protein where theantibody specifically binds to the truncation mutant of BCR-ABL protein(e.g. Del 2595-2779, Del 2596-2597, 2417insCAGG, C2506T) and not to aBCR-ABL protein without such mutation. In one example, the antibodyspecifically binds to an epitope comprising SEQ ID NO: 11, 16, or 20.

Also provided herein is a vector including a recombinant polynucleotide,in which the recombinant polynucleotide having at least 50 contiguousnucleotides selected from the group consisting of SEQ ID NO: 3, 7, 12,and 17 or their complements. In one example, the polynucleotide isoperably linked to an expression regulatory element, in which theexpression regulatory element is capable of modulating the expression ofsaid recombinant polynucleotide.

Also provided are genetically modified cells which include a recombinantnucleic acid, in which the recombinant nucleic acid that includes thenucleic acid sequence of the one or more of the BCR-ABL truncationmutations or their complements. In some examples, the geneticallymodified cells include a recombinant nucleic acid having a nucleotidesequence of SEQ ID NO: 3, SEQ ID NO: 7, SEQ ID NO: 12, or SEQ ID NO: 17.Also included are genetically modified cells that contain vectorscomprising the nucleic acid sequences described above. In some examplesthe recombinant polynucleotide is a cDNA construct while in otherexamples, the recombinant polynucleotide is genomic construct. In someexamples, the genetically modified cells are eukaryotic. In someexamples, the recombinant polypeptide has kinase activity.

Also provided are methods of identifying a compound for treating apatient diagnosed as having a myeloproliferative disease, includingcontacting genetically modified cells with a candidate compound, andassessing the effect of the candidate compound on the cells, in whichthe candidate compound is identified as a compound for treating apatient with the myeloproliferative disease when the effect of thecandidate compound on the genetically modified cells is beneficial inthe treatment of the myeloproliferative disease. In some examples, thecandidate compound is a protein kinase inhibitor. In some examples, thecandidate compound is an inhibitor for BCR-ABL. In some examples, thecandidate compound is selected from the group consisting of imatinib,dasatinib, bosutinib, and nilotinib.

In one example, the effect of the compound on the cells is a reductionin the viability or growth rate of the cells or reduction of at leastone activity of the expressed recombinant polypeptide. In one example,the effect is a reduction in the viability of the genetically modifiedcells. In another example, the reduction in viability is reflected by anincrease in apoptosis of the genetically modified cells. In one example,the effect is the effect on the kinase activity of the expressedrecombinant polypeptide. In one example, the kinase activity isdetermined by testing the phosphorylation status of a substrate ofBCR-ABL. In another example, the effect is a reduction in growth rate ofthe cells. In one example, the growth rate is measured by the amount ofDNA synthesis. In one example, the cells are resistant to imatinib. Inone example, the cells are CIVIL cells. In one example, the CIVIL cellsare K562 cells.

In some examples, the presence or absence of the polypeptide isdetermined by assessing the size of the BCR-ABL protein. In anotherexample, the presence or absence of the polypeptide is determined bywestern blotting. In another example, the presence or absence of thepolypeptide is determined by flow cytometry. In some examples, themethod simultaneously detects wild-type BCR-ABL protein and thetruncation mutant of BCR-ABL protein.

As used herein, the term “subject” or “individual” refers to a human orany other animal that has cells that may contain a BCR-ABLtranslocation. A subject can be a patient, which refers to a humanpresenting to a medical provider for diagnosis or treatment of adisease. A human includes pre and post natal forms.

As used herein, the term “patient” refers to one who receives medicalcare, attention or treatment. As used herein, the term is meant toencompass a person diagnosed with a disease as well as a person who maybe symptomatic for a disease but who has not yet been diagnosed.

As used herein, the term “sample” refers to any liquid or solid materialobtained from an individual that contains nucleic acids and/or proteins.In preferred examples, a patient sample is obtained from a biologicalsource (i.e., a “biological sample”), such as cells in culture, bodilyfluids or a tissue sample from an animal, more preferably, a human.“Bodily fluids” may include, but are not limited to, blood, serum,plasma, saliva, cerebral spinal fluid, pleural fluid, tears, lactal ductfluid, lymph, sputum, urine, amniotic fluid, and semen. A sample mayinclude a bodily fluid that is “acellular.” An “acellular bodily fluid”includes less than about 1% (w/w) whole cellular material. Plasma orserum are examples of acellular bodily fluids. A sample may include aspecimen of natural or synthetic origin.

As used herein, the term “nucleic acid” or “nucleic acid sequence”refers to an oligonucleotide, nucleotide or polynucleotide, andfragments or portions thereof, which may be single or double stranded,or partially double stranded and represent the sense or antisensestrand. A nucleic acid may include DNA or RNA, and may be of natural orsynthetic origin and may contain deoxyribonucleotides, ribonucleotides,or nucleotide analogs in any combination. Nucleic acid may comprise adetectable label. Although a sequence of the nucleic acids may be shownin the form of DNA, a person of ordinary skill in the art recognizesthat the corresponding RNA sequence will have a similar sequence withthe thymine being replaced by uracil i.e. “t” with “u”.

Non-limiting examples of nucleic acid include a gene or gene fragment,genomic DNA, exons, introns, mRNA, tRNA, rRNA, ribozymes, cDNA,recombinant nucleic acid, branched nucleic acid, plasmids, vectors,isolated DNA of any sequence, isolated RNA of any sequence, syntheticnucleic acid, nucleic acid probes and primers. Nucleic acid may comprisemodified nucleotides, such as methylated nucleotides and nucleotideanalogs, uracyl, other sugars and linking groups such as fluororiboseand thiolate, and nucleotide branches. A nucleic acid may be modifiedsuch as by conjugation, with a labeling component. Other types ofmodifications included in this definition are caps, substitution of oneor more of the naturally occurring nucleotides with an analog, andintroduction of chemical entities for attaching the polynucleotide toother molecules such as proteins, metal ions, labeling components, othernucleic acid or a solid support. Nucleic acid may include nucleic acidthat has been amplified (e.g., using polymerase chain reaction).

A fragment of a nucleic acid generally contains at least about 15, 20,25, 30, 35, 40, 45, 50, 75, 100, 200, 300, 400, 500, 1000 nucleotides ormore. Larger fragments are possible and may include about 2,000, 2,500,3,000, 3,500, 4,000, 5,000 7,500, or 10,000 bases.

A fragment of a polypeptide generally contains at least about 5, 10, 15,20, 25, 30, 35, 40, 45, 50, 75, 100, 200, 300, 400, 500, 1000 aminoacids or more. Larger fragments are possible and may include about 1200,1500 or more amino acids.

As used herein, the term “wild-type” refers to a gene or a gene productthat has the characteristics of that gene or gene product when isolatedfrom a naturally occurring source. A wild-type gene is that which ismost frequently observed in a population and is thus arbitrarilydesignated the “normal” or “wild-type” form of the gene. “Wild-type” mayalso refer to the sequence at a specific nucleotide position orpositions, or the sequence at a particular codon position or positions,or the sequence at a particular amino acid position or positions.

As used herein, the term “mutant” or “modified” refers to a gene or geneproduct which displays modifications in sequence and or functionalproperties (i.e., altered characteristics) when compared to thewild-type gene or gene product. “Mutant” or “modified” also refers tothe sequence at a specific nucleotide position or positions, or thesequence at a particular codon position or positions, or the sequence ata particular amino acid position or positions which displaysmodifications in sequence and or functional properties (i.e., alteredcharacteristics) when compared to the wild-type gene or gene product.

As used herein, the term “mutation” refers to a nucleic acid with atleast a single nucleotide variation relative to the normal sequence orwild-type sequence. In the context of polypeptide, “mutation” refers toat least a single amino acid variation in a polypeptide sequencerelative to the normal sequence or wild-type sequence. A mutation mayinclude a substitution, a deletion, an inversion or an insertion. Withrespect to an encoded polypeptide, a mutation may be “silent” and resultin no change in the encoded polypeptide sequence or a mutation mayresult in a change in the encoded polypeptide sequence. For example, amutation may result in a substitution in the encoded polypeptidesequence. A mutation may result in a frameshift with respect to theencoded polypeptide sequence.

As used herein, the convention “NTwt###NTmut” is used to indicate amutation that results in the wild-type nucleotide NTwt at position ###in the nucleic acid being replaced with mutant NTmut. As used herein,the convention “AAwt###AAmut” is used to indicate a mutation thatresults in the wild-type amino acid AAwt at position ### in thepolypeptide being replaced with mutant AAmut.

As used herein, the terms “protein,” “peptide,” “polypeptide,” and“polypeptide fragment” are used interchangeably to refer to polymers ofamino acids (“an amino acid sequence”) of any length. The polymer can belinear or branched, it may comprise modified amino acids or amino acidanalogs, and it may be interrupted by chemical moieties other than aminoacids. The terms also encompass an amino acid polymer that has beenmodified naturally or by intervention; for example disulfide bondformation, glycosylation, lipidation, acetylation, phosphorylation, orany other manipulation of modification, such as conjugation with alabeling or bioactive component.

As used herein, the terms “identity” and “identical” refer to a degreeof identity between sequences. There may be partial identity or completeidentity. A partially identical sequence is one that is less than 100%identical to another sequence. Preferably, partially identical sequenceshave an overall identity of at least 70% or at least 75%, morepreferably at least 80% or at least 85%, most preferably at least 90% orat least 95% or at least 99%. Sequence identity determinations may bemade for sequences which are not fully aligned. In such instances, themost related segments may be aligned for optimal sequence identity byand the overall sequence identity reduced by a penalty for gaps in thealignment.

The term “substantially identical” in the context of polynucleotides andmeans at least 65%, at least 70% or at least 75%, at least 80% or atleast 85%, at least 90%, at least 95%, at least 99% or identical.

As used herein, the term “insertion” or “addition” refers to a change inan amino acid or nucleotide sequence resulting in the addition of one ormore amino acid residues or nucleotides respectively, as compared to thenaturally occurring molecule.

As used herein, the term “truncation” refers to a shortening in theamino acid sequence of protein or the nucleotide sequence of a nucleicacid or segment of a nucleic acid (e.g., a gene). A protein truncationmay be the result of a truncation in the nucleic acid sequence encodingthe protein, a substitution or other mutation that creates a prematurestop codon without shortening the nucleic acid sequence, or fromalternate splicing of RNA in which a substitution or other mutation thatdoes not itself cause a truncation results in aberrant RNA processing.

As used herein, the term “truncation mutation” or “truncation mutant” inthe context of BCR-ABL nucleic acid refers to a BCR-ABL nucleic acidlacking one or more nucleotides relative to the nucleic acid sequence ofSEQ ID NO: 1 such that the BCR-ABL protein encoded by the nucleic acidwill have truncated C-terminus as compared to SEQ ID NO: 2. Exemplarytruncation mutation of BCR-ABL nucleic acid includes but are not limitedto Del 2595-2779, Del 2596-2597, 2417insCAGG, and C2506T.

As used herein, the term “truncation mutation” or “truncation mutant” inthe context of BCR-ABL protein refers to a BCR-ABL protein with adeletion of one or more amino acids at the C-terminal region of theprotein as compared to the exemplary reference BCR-ABL protein aminoacid sequence of SEQ ID NO: 2. In preferred examples, such truncationmutation may result from deletion of nucleotides 2595-2779 (Del2595-2779), insertion of CAGG immediately after nucleotide 2417(2417insCAGG), GA deletion at position 2596-2597 (Del 2596-2597), andsubstitution of C to T at nucleotide position 2506 (C2506T) of SEQ IDNO: 1.

Several variants of BCR-ABL protein without truncation mutation areknown in the art. Exemplary BCR-ABL protein sequences include but arenot limited to NCBI protein database accession numbers: ABX82708,ABX82702, and AAA35594.

As used herein, the term “hybridize” or “hybridization” refers to thepairing of substantially complementary nucleotide sequences (strands ofnucleic acid) to form a duplex or heteroduplex through formation ofhydrogen bonds between complementary base pairs. Hybridization and thestrength of hybridization (i.e., the strength of the association betweenthe nucleic acids) is influenced by such factors as the degree ofcomplementary between the nucleic acids, stringency of the conditionsinvolved, and the T. of the formed hybrid. An oligonucleotide orpolynucleotide (e.g., a probe or a primer) that is specific for a targetnucleic acid will “hybridize” to the target nucleic acid under suitableconditions. See e.g., Sambrook, et al., Molecular Cloning: A LaboratoryManual, Second Edition (1989), Cold Spring Harbor Press, Plainview, N.Y.

As used herein, the term “specific hybridization” refers to anindication that two nucleic acid sequences share a high degree ofcomplementarity. Specific hybridization complexes form under permissiveannealing conditions and remain hybridized after any subsequent washingsteps. Permissive conditions for annealing of nucleic acid sequences areroutinely determinable by one of ordinary skill in the art and mayoccur, for example, at 65° C. in the presence of about 6×SSC. Stringencyof hybridization may be expressed, in part, with reference to thetemperature under which the wash steps are carried out. Suchtemperatures are typically selected to be about 5° C. to 20° C. lowerthan the thermal melting point (Tm) for the specific sequence at adefined ionic strength and pH. The Tm is the temperature (under definedionic strength and pH) at which 50% of the target sequence hybridizes toa perfectly matched probe. Equations for calculating Tm and conditionsfor nucleic acid hybridization are known in the art.

As used herein, the term “stringent hybridization conditions” refers tohybridization conditions at least as stringent as the following:hybridization in 50% formamide, 5×SSC, 50 mM NaH₂PO₄, pH 6.8, 0.5% SDS,0.1 mg/mL sonicated salmon sperm DNA, and 5× Denhart's solution at 42°C. overnight; washing with 2×SSC, 0.1% SDS at 45° C.; and washing with0.2×SSC, 0.1% SDS at 45° C. In another example, stringent hybridizationconditions should not allow for hybridization of two nucleic acids whichdiffer over a stretch of 20 contiguous nucleotides by more than twobases.

As used herein, the term “substantially complementary” refers to twosequences that hybridize under stringent hybridization conditions. Theskilled artisan will understand that substantially complementarysequences need not hybridize along their entire length.

As used herein, the term “oligonucleotide” as used herein refers to amolecule that has a sequence of nucleic acid bases on a backbonecomprised mainly of identical monomer units at defined intervals. Thebases are arranged on the backbone in such a way that they can enterinto a bond with a nucleic acid having a sequence of bases that arecomplementary to the bases of the oligonucleotide. The most commonoligonucleotides have a backbone of sugar phosphate units. A distinctionmay be made between oligodeoxyribonucleotides that do not have ahydroxyl group at the 2′ position and oligoribonucleotides that have ahydroxyl group in this position. Oligonucleotides also may includederivatives, in which the hydrogen of the hydroxyl group is replacedwith organic groups, e.g., an allyl group. Oligonucleotides of themethods which function as primers or probes are generally at least about10 to 15 nucleotides long and more preferably at least about 15 to 25nucleotides long, although shorter or longer oligonucleotides may beused in the method. The exact size will depend on many factors, which inturn depend on the ultimate function or use of the oligonucleotide. Theoligonucleotide may be generated in any manner, including, for example,chemical synthesis, DNA replication, reverse transcription, PCR, or acombination thereof. The oligonucleotide may be modified. For example,the oligonucleotide may be labeled with an agent that produces adetectable signal (e.g., a fluorophore). Oligonucleotides can be used asprimers or probes for specifically amplifying (i.e., amplifying aparticular target nucleic acid sequence) or specifically detecting(i.e., detecting a particular target nucleic acid sequence) a targetnucleic acid generally are capable of specifically hybridizing to thetarget nucleic acid.

As used herein, the term “primer” refers to an nucleic acid that iscapable of acting as a point of initiation of synthesis when placedunder conditions in which primer extension is initiated (e.g., primerextension associated with an application such as PCR). The primer iscomplementary to a target nucleotide sequence and it hybridizes to asubstantially complementary sequence in the target and leads to additionof nucleotides to the 3″-end of the primer in the presence of a DNA orRNA polymerase. The 3′-nucleotide of the primer should generally becomplementary to the target sequence at a corresponding nucleotideposition for optimal expression and amplification. An oligonucleotide“primer” may occur naturally, as in a purified restriction digest or maybe produced synthetically. The term “primer” includes all forms ofprimers that may be synthesized including peptide nucleic acid primers,locked nucleic acid primers, phosphorothioate modified primers, labeledprimers, and the like. Primers are typically between about 10 and about100 nucleotides in length, preferably between about 15 and about 60nucleotides in length, more preferably between about 20 and about 50nucleotides in length, and most preferably between about 25 and about 40nucleotides in length. In some examples, primers can be at least 8, atleast 12, at least 16, at least 20, at least 25, at least 30, at least35, at least 40, at least 45, at least 50, at least 55, at least 60nucleotides in length. An optimal length for a particular primerapplication may be readily determined in the manner described in H.Erlich, PCR Technology, Principles and Application for DNA Amplification(1989).

As used herein, the term “probe” refers to nucleic acid that interactswith a target nucleic acid via hybridization. A probe may be fullycomplementary to a target nucleic acid sequence or partiallycomplementary. The level of complementarity will depend on many factorsbased, in general, on the function of the probe. A probe or probes canbe used, for example to detect the presence or absence of a mutation ina nucleic acid sequence by virtue of the sequence characteristics of thetarget. Probes can be labeled or unlabeled, or modified in any of anumber of ways well known in the art. A probe may specifically hybridizeto a target nucleic acid. Probes may be DNA, RNA or a RNA/DNA hybrid.Probes may be oligonucleotides, artificial chromosomes, fragmentedartificial chromosome, genomic nucleic acid, fragmented genomic nucleicacid, RNA, recombinant nucleic acid, fragmented recombinant nucleicacid, peptide nucleic acid (PNA), locked nucleic acid, oligomer ofcyclic heterocycles, or conjugates of nucleic acid. Probes may comprisemodified nucleobases, modified sugar moieties, and modifiedinternucleotide linkages. A probe may be fully complementary to a targetnucleic acid sequence or partially complementary. A probe may be used todetect the presence or absence of a target nucleic acid. Probes aretypically at least about 10, 15, 20, 25, 30, 35, 40, 50, 60, 75, 100nucleotides or more in length.

As used herein, the term “detectable label” refers to a molecule or acompound or a group of molecules or a group of compounds used toidentify a nucleic acid or protein of interest. In some cases, thedetectable label may be detected directly. In other cases, thedetectable label may be a part of a binding pair, which can then besubsequently detected. Signals from the detectable label may be detectedby various means and will depend on the nature of the detectable label.Detectable labels may be isotopes, fluorescent moieties, coloredsubstances, and the like. Examples of means to detect detectable labelinclude but are not limited to spectroscopic, photochemical,biochemical, immunochemical, electromagnetic, radiochemical, or chemicalmeans, such as fluorescence, chemifluoresence, or chemiluminescence, orany other appropriate means.

As used herein, the term “promoter” refers to a segment of DNA thatcontrols transcription of polynucleotide to which it is operativelylinked. Promoters, depending upon the nature of the regulation, may beconstitutive or regulated. Exemplary eukaryotic promoters contemplatedfor use include the SV40 early promoter, the cytomegalovirus (CMV)promoter, the mouse mammary tumor virus (MMTV) steroid-induciblepromoter, Moloney murine leukemia virus (MMLV) promoter. Exemplarypromoters suitable for use with prokaryotic hosts include T7 promoter,beta-lactamase promoter, lactose promoter systems, alkaline phosphatasepromoter, a tryptophan (trp) promoter system, and hybrid promoters suchas the tac promoter.

As used herein, the term “antibody” refers to a polypeptide, at least aportion of which is encoded by at least one immunoglobulin gene, orfragment thereof, and that can bind specifically to a desired targetmolecule. The term includes naturally-occurring forms, as well asfragments and derivatives. Fragments within the scope of the term“antibody” include those produced by digestion with various proteases,those produced by chemical cleavage and/or chemical dissociation, andthose produced recombinantly, so long as the fragment remains capable ofspecific binding to a target molecule. Among such fragments are Fab,Fab′, Fv, F(ab)′₂, and single chain Fv (scFv) fragments. Derivativeswithin the scope of the term include antibodies (or fragments thereof)that have been modified in sequence, but remain capable of specificbinding to a target molecule, including: interspecies chimeric andhumanized antibodies; antibody fusions; heteromeric antibody complexesand antibody fusions, such as diabodies (bispecific antibodies),single-chain diabodies, and intrabodies (see, e.g., Marasco (ed.),Intracellular Antibodies: Research and Disease Applications,Springer-Verlag New York, Inc. (1998) (ISBN: 3540641513). As usedherein, antibodies can be produced by any known technique, includingharvest from cell culture of native B lymphocytes, harvest from cultureof hybridomas, recombinant expression systems, and phage display.

As used herein, the term “specifically binds to an epitope” in thecontext of an antibody refers to an antibody that specifically binds toBCR-ABL truncation mutants of BCR-ABL protein and does not bind toBCR-ABL proteins without such truncation mutation and thus candistinguish between BCR-ABL proteins with and without truncationmutation. In some examples, the antibodies specific for BCR-ABLtruncation mutants binds to an amino acid sequence comprising SEQ ID NO:6, 10, 15 or 19. In one example, the antibodies specific for BCR-ABLtruncation mutants binds to an epitope comprising SEQ ID NO's 11, 16, or20. In one example, the antibodies specific for BCR-ABL truncationmutants binds to BCR-ABL proteins having amino acid sequences of SEQ IDNO: 5, 9, 14 or 19.

As used herein, the term “myeloproliferative disease” or“myeloproliferative disorder” or “MPD” is meant to include non-lymphoiddysplastic or neoplastic conditions arising from a hematopoietic stemcell or its progeny. “MPD patient” or “myeloproliferative diseasepatient” refers to a patient diagnosed with a myeloproliferative diseaseor suspected of having a myeloproliferative disease. One of ordinaryskill in the art is capable of diagnosing a myeloproliferative diseaseusing suitable diagnostic criteria. “Myeloproliferative disease” ismeant to encompass the specific, classified types of myeloproliferativediseases including chronic myelogenous leukemia (CML), acute myelogenousleukemia (AML), acute lymphoblastic leukemia (ALL), polycythemia vera(PV), essential thrombocythemia (ET) and idiopathic myelofibrosis (IMF).Also included in the definition are hypereosinophilic syndrome (HES),chronic neutrophilic leukemia (CNL), myelofibrosis with myeloidmetaplasia (MMM), chronic myelomonocytic leukemia (CMML), juvenilemyelomonocytic leukemia, chronic basophilic leukemia, chroniceosinophilic leukemia, and systemic mastocytosis (SM).“Myeloproliferative disease” is also meant to encompass any unclassifiedmyeloproliferative diseases (UMPD or MPD-NC).

As used herein, the term “kinase domain” refers to a portion of apolypeptide or nucleic acid that encodes a portion of the polypeptide,where the portion is required for kinase activity of the polypeptide(e.g., tyrosine kinase activity).

As used herein, the term “diagnose” or “diagnosis” or “diagnosing” referto distinguishing or identifying a disease, syndrome or condition ordistinguishing or identifying a person having a particular disease,syndrome or condition. Usually, a diagnosis of a disease or disorder isbased on the evaluation of one or more factors and/or symptoms that areindicative of the disease. That is, a diagnosis can be made based on thepresence, absence or amount of a factor which is indicative of presenceor absence of the disease or condition. Each factor or symptom that isconsidered to be indicative for the diagnosis of a particular diseasedoes not need be exclusively related to the particular disease; i.e.there may be differential diagnoses that can be inferred from adiagnostic factor or symptom. Likewise, there may be instances where afactor or symptom that is indicative of a particular disease is presentin an individual that does not have the particular disease.

As used herein, the term “treatment,” “treating,” or “treat” refers tocare by procedures or application that are intended to relieve illnessor injury. Although it is preferred that treating a condition or diseasewill result in an improvement of the condition, the term treating asused herein does not indicate, imply, or require that the procedures orapplications are at all successful in ameliorating symptoms associatedwith any particular condition. Treating a patient may result in adverseside effects or even a worsening of the condition which the treatmentwas intended to improve.

As used herein, the term “altering the treatment” in reference to apatient includes, but is not limited to, adding a new drug to treatmentregime, removing a drug from the treatment regime, changing dosage of adrug. In one example, the term refers to ceasing the use of imatinib ina myeloproliferative disease patient undergoing imatinib therapy. Inother examples, the term refers to bone marrow transplant.

The term “prognosis” as used herein refers to a prediction of theprobable course and outcome of a clinical condition or disease. Aprognosis is usually made by evaluating factors or symptoms of a diseasethat are indicative of a favorable or unfavorable course or outcome ofthe disease. There are many ways that prognosis can be expressed. Forexample prognosis can be expressed in terms of complete remission rates(CR), overall survival (OS) which is the amount of time from entry todeath, remission duration, which is the amount of time from remission torelapse or death.

The phrase “determining the prognosis” as used herein refers to theprocess by which the practitioner can predict the course or outcome of acondition in an individual. The term “prognosis” does not refer to theability to predict the course or outcome of a condition with 100%accuracy. Instead, the skilled artisan will understand that the term“prognosis” refers to an increased probability that a certain course oroutcome will occur; that is, that a course or outcome is more likely tooccur in a patient exhibiting a given condition, when compared to thoseindividuals not exhibiting the condition. A prognosis may be expressedas the amount of time a patient can be expected to survive.Alternatively, a prognosis may refer to the likelihood that the diseasegoes into remission or to the amount of time the disease can be expectedto remain in remission. Prognosis can be expressed in various ways; forexample prognosis can be expressed as a percent chance that a patientwill survive after one year, five years, ten years or the like.Alternatively prognosis may be expressed as the number of years, onaverage that a patient can expect to survive as a result of a conditionor disease. The prognosis of a patient may be considered as anexpression of relativism, with many factors affecting the ultimateoutcome. For example, for patients with certain conditions, prognosiscan be appropriately expressed as the likelihood that a condition may betreatable or curable, or the likelihood that a disease will go intoremission, whereas for patients with more severe conditions prognosismay be more appropriately expressed as likelihood of survival for aspecified period of time.

As used herein, the term “poor prognosis” refers a the prognosisdetermined for a patient having a myeloproliferative disease which isworse (i.e., has a less favorable outcome) than the prognosis for areference patient or group of patients with the same disease. Forexample, a patient with a poor prognosis may be expected to exhibit areduced remission duration or survival time relative to referencepatients (e.g., patients without one of the BCR-Abl truncation mutationsdescribed herein).

As used herein, the term “isolated” when referring to a nucleic acid orprotein molecule means that the molecule is apart from its naturalenvironment and/or is substantially separated from other cellularcomponents which naturally accompany such molecule. For example, anynucleic acid or protein that has been produced synthetically (e.g., byserial base condensation) is considered to be isolated. Likewise,nucleic acids or proteins that are recombinantly expressed, cloned,produced by a synthetic in vitro reaction are considered to be isolated.An isolated nucleic acid or protein is at least 25% free, preferably atleast 30% free, preferably at least 40% free, preferably at least 50%free, preferably at least 60% free, more preferably at least 75% free,and most preferably at least 90% free from other components with whichit is naturally associated.

The term “substantially all” as used herein means at least about 60%,about 70%, about 80%, about 90%, about 95%, about 99%, or 100%.

“Substantially pure” as used herein in the context of nucleic acidrepresents at least 50%, at least 60%, at least 70%, at least 80%, atleast 90%, at least 95% or at least 99% of the nucleic acid in a sample.The nucleic acid sample may exist in solution or as a dry preparation.As used herein, the term “including” has the same meaning as the termcomprising.

As used herein, the term “about” means in quantitative terms, plus orminus 10%.

As used herein “portions of” in the context of nucleic acid means atleast about 10, 20, 30, 40, 50, 60, 75, 100, 200, 500, 1000, 2000, 3000or more nucleotides.

BRIEF DESCRIPTION OF FIGURES

FIG. 1. shows a schematic diagram of BCR-ABL protein. Different domainsof BCR-ABL protein are indicated. BCR: portions of BCR protein, SH2 andSH3: Src homology domains 2 and 3 respectively, P: proline rich region,NLS: nuclear localization signal, DB: DNA-binding domain, AB:Actin-binding domain.

FIGS. 2A-2D show the chromatograms of sequencing BCR-ABL cDNA variants.FIG. 2A: Del 2595-2779, FIG. 2B: Del 2596-2597, FIG. 2C: 2417insCAGG,FIG. 2D: C2506T. FIG. 2E shows an exemplary sequence analysis of Del2595-2779 sequence by ABI Prism® SeqScape software.

FIGS. 3A-3B show maps of expression vectors comprising BCR-ABL wild typeand its truncation mutation variants.

DETAILED DESCRIPTION OF THE INVENTION

Provided herein are methods and compositions related to mutations thatencode a C-terminal truncated BCR-ABL protein that renders cellsresistant to treatment with kinase domain inhibitors such as imatinib.In some examples, increasing amounts of the truncation mutant correlatedirectly with resistance. The inventions described herein includenucleic acid which encode all or portions of the truncation variant andcells that express all or portions of the truncation variant. Methodsfor predicting likelihood for responsiveness to kinase inhibitor therapyare included along with methods, compositions and reagents for detectingthe truncation variant.

Variants of the BCR-ABL mRNA

Several variants of BCR-ABL mRNA have been reported. Many of the knownsequences are full length cDNA sequences and some are partial cDNAsequences. Exemplary BCR-ABL mRNA sequences include but are not limitedto: NCBI GenBank accession numbers: EU 216060, EU216072, EU216071,EU216070, EU216069, EU216068, EU216067, EU216066, EU216065, EU216064,EU216063, EU216062, EU216061, EU216060, EU216059, EU216058, EU236680,DQ912590, DQ912589, DQ912588, DQ898315, DQ898314, DQ898313, EF423615,EF158045, 572479, 572478, AY789120, AB069693, AF487522, AF113911,AF251769, M30829, M30832, M17542, M15025, and M17541. The nucleic acidsequences are incorporated herein by reference. An exemplary cDNAsequence of BCR-ABL cDNA is listed as SEQ ID NO: 1.

Variants of BCR-ABL Protein

Several variation of BCR-ABL protein sequence is known in the art. Someof the amino acid sequences are for full length protein and some areamino acid sequences for a fragment of BCR-ABL protein. ExemplaryBCR-ABL protein sequence include but not limited to the NCBI proteindatabase accession numbers: ABX82708, ABX82702, AAA35594, ACA62749,ABX82713, CAM33013, CAA10377, CAA10376, AAL99544, AAA88013, CAM33009,ABX82714, ABX82712, ABX82711, ABX82710, ABX82709, ABX82707, ABX82706,ABX82705, ABX82704, ABX82703, ABX82701, ABX82700, ABZ01959, ABW90981,AAL05889, AAA87612, CAM33011, CAP08044, ABM21758, AAD04633, AAF89176,ABZ01958, AB009836, ABZ01957, ABK56838, ABK56837, ABK56836, ABK19807,ABK19806, ABK19805, AAA35596, AAF61858, AAA35595, AAA35592. Sequences ofthe above proteins are incorporated herein by reference.

Exemplary amino acid sequence of full length BCR-ABL protein without anyinsertion or truncation mutation is listed in SEQ ID NO: 2. A schematicdiagram of BCR-ABL protein showing the different domains is shown inFIG. 1. The domains include a portion of BCR protein, Src homologydomains 2 and 3 (SH2 and SH3), proline rich regions (P), nuclearlocalization signal (NLS), and DNA- and Actin-binding domains DB and ABrespectively.

Truncation Mutant of BCR-ABL Protein:

In some examples, myeloproliferative disease patients undergoing BCR-ABLtyrosine kinase inhibitor therapy (for example, imatinib, nilotinib,Bosutinib (SKI-606) and Aurora kinase inhibitor VX-680, or dasatinib),may subsequently acquire a mutation that affects the effectiveness ofthe tyrosine kinase inhibitor. The mutation may be a large deletion ofnucleotides 2595-2779 of SEQ ID NO: 1, or an insertion oftetranucleotide CAGG at nucleotide position immediately after nucleotide2417 of SEQ ID NO: 1, or a deletion of “GA” at position 2596-2597 of SEQID NO: 1, or a C to T substitution at position 2506 of SEQ ID NO: 1.These mutations cause truncation of a portion of kinase domain, abolishregulatory element in the ABL kinase domain and the downstreamC-terminal region (such as, NLS, P, AB, DB domains) and conferresistance to kinase inhibitors such as imatinib, nilotinib, dasatinib,Bosutinib (SKI-606) and Aurora kinase inhibitor VX-680. Deletion ofactin-binding domain or the entire C-terminal domain induces CIVIL-likemyeloproliferative disorder in mice (Wertheim et al. Blood. 2003; 102:2220-2228). The truncated proteins resulting from premature translationtermination are expected to possess leukomogenic activity and to induceconformational change to confer drug resistance to kinase inhibitors.

Del 2595-2779

The deletion of nucleotides 2595-2779 results in a truncated BCR-ABLprotein with a new C-terminal region for the BCR-ABL protein. Exemplarynucleic acid sequence of BCR-ABL Del 2595-2779 is listed as SEQ ID NO:3. In some examples, the nucleic acid encoding the BCR-ABL Del 2595-2779mRNA or cDNA, its fragments and complements thereof may include thedeletion junction “GC” (nucleotides 2594 and 2595 of SEQ ID NO: 3) thatis at least 95%, at least 99% identical or identical to at least 25, atleast 26, at least 27, at least 28, or 29 contiguous nucleotides of SEQID NO: 4. Sequence of SEQ ID NO: 4 is shown below.

(SEQ ID NO: 4) AACTTCATCCACAGCATTTGGAGTATTGC

The truncated BCR-ABL protein includes BCR portion of BCR-ABL protein,SH3 and SH2 domains and a portion of kinase domain. However thetruncated protein lacks the P, NLS, DB and AB domains. Additionally, theC-terminus of the truncated BCR-ABL protein will comprise new aminoacids. Exemplary amino acid sequence of the truncation mutant of BCR-ABLprotein is listed as SEQ ID NO: 5. In preferred examples, C-terminalregion of the BCR-ABL protein encoded by the BCR-ABL Del 2595-2779 mRNAmay comprise a sequence of at least 75%, at least 80%, at least 85%, atleast 90%, at least 99%, or identical to at least 15 contiguous aminoacids of SEQ ID NO: 6. Sequence of SEQ ID NO: 6 is shown below.

(SEQ ID NO: 6) EYLEKKNFIHSIWSIALGNCYLWHVPLPGN

In one example, the new amino acid sequence generated at the C-terminusof the truncated protein encoded by BCR-ABL Del 2595-2779 mRNA is:

(SEQ ID NO: 20) SIWSIALGNCYLWHVPLPGN

Del 2596-2597

The Del 2596-2597 mutation is a deletion of 2 nucleotides “GA” atposition 2597-2597 of the BCR-ABL gene resulting in a truncated BCR-ABLprotein with a new C-terminal region for the BCR-ABL protein. Exemplarynucleic acid sequence of BCR-ABL Del 2596-2597 is listed as SEQ ID NO:7. In some examples, the nucleic acid encoding the BCR-ABL Del 2596-2597mRNA or cDNA, its fragments and complements thereof may include thedeletion junction “AT” (nucleotides 2595 and 2596 of SEQ ID NO: 7) thatis at least 95%, at least 99% identical or identical to at least 20, atleast 25, or 30 contiguous nucleotides of SEQ ID NO: 8. Sequence of SEQID NO: 8 is shown below.

(SEQ ID NO: 8) AACTTCATCCACAGATCTTGCTGCCCGAAA

The truncated BCR-ABL protein includes BCR portion of BCR-ABL protein,SH3 and SH2 domains and a portion of kinase domain. However thetruncated protein lacks the P, NLS, DB and AB domains. Additionally, theC-terminus of the truncated BCR-ABL protein will comprise new aminoacids. Exemplary amino acid sequence of the truncation mutant of BCR-ABLprotein is listed as SEQ ID NO: 9. In preferred examples, C-terminalregion of the BCR-ABL protein encoded by the BCR-ABL Del 2596-2597 mRNAmay comprise a sequence of at least 85%, at least 90%, at least 95%, atleast 99%, or identical to at least 20 contiguous amino acids of SEQ IDNO: 10. Sequence of SEQ ID NO: 10 is shown below.

(SEQ ID NO: 10) SSAMEYLEKKNFIHRSCCPKLPGRGEPLGEGS

In one example, the new amino acid sequence generated at the C-terminusof the truncated protein encoded by BCR-ABL Del 2596-2597 mRNA is:

(SEQ ID NO: 11) SCCPKLPGRGEPLGEGS

2417insCAGG

The 2417insCAGG mutation is an insertion of tetranucleotide CAGGimmediately after nucleotide position 2417 of SEQ ID NO: 1 resulting ina truncated BCR-ABL protein with a new C-terminal region for the BCR-ABLprotein. Exemplary nucleic acid sequence of BCR-ABL 2417insCAGG islisted as SEQ ID NO: 12. In some examples, the nucleic acid encodingBCR-ABL 2417insCAGG mRNA or cDNA, its fragments and complements thereofmay include the CAGG insert that is at least 95%, at least 99% identicalor identical to at least 25 or 30 contiguous nucleotides of SEQ ID NO:13. Sequence of SEQ ID NO: 13 is shown below.

(SEQ ID NO: 13) CTGGTGCAGCTCCTTGGCAGGGGTCTGCAC

The truncated BCR-ABL protein encoded by BCR-ABL 2417insCAGG mRNAincludes BCR portion of BCR-ABL protein, SH3 and SH2 domains and aportion of kinase domain. However the truncated protein lacks the P,NLS, DB and AB domains. Additionally, the C-terminus of the truncatedBCR-ABL protein will comprise new amino acids. Exemplary amino acidsequence of the truncation mutant of BCR-ABL protein is listed as SEQ IDNO: 14. In some examples, C-terminal region of the BCR-ABL proteinencoded by the BCR-ABL 2417insCAGG mRNA may comprise a sequence of atleast 75%, at least 80%, at least 85%, at least 90%, at least 95%, atleast 99%, or identical to least 20 contiguous amino acids of SEQ ID NO:15. Sequence of SEQ ID NO: 15 is shown below.

(SEQ ID NO: 15) AVMKEIKHPNLVQLLGRGLHPGAPVLYHEI

In one example, the new amino acid sequence generated at the C-terminusof the truncated protein encoded by BCR-ABL 2417insCAGG mRNA is:

(SEQ ID NO: 16) RGLHPGAPVLYHH

C2506T

The C2506T mutation is a single base substitution at position 2506 ofSEQ ID NO: 1 resulting in a truncated BCR-ABL protein with a newC-terminal region for the BCR-ABL protein. Exemplary nucleic acidsequence of BCR-ABL C2506T is listed as SEQ ID NO: 17. In some examples,the nucleic acid encoding the BCR-ABL C2506T mRNA or cDNA, its fragmentsand complements thereof may include a “C” to “T” at nucleotide position2506 of SEQ ID NO: 1 that is at least 95%, at least 99% identical oridentical to at least 20 or 30 contiguous nucleotides of SEQ ID NO: 18.Sequence of SEQ ID NO: 18 is shown below.

(SEQ ID NO: 18) AGGGAGTGCAACCGGTAGGAGGTGAACGCC

The truncated BCR-ABL protein encoded by BCR-ABL C2506T mRNA includesBCR portion of BCR-ABL protein, SH3 and SH2 domains and a portion ofkinase domain. However the truncated protein lacks the P, NLS, DB and ABdomains. Exemplary amino acid sequence of the truncation mutant ofBCR-ABL protein is listed as SEQ ID NO: 19. In preferred examples,C-terminal region of the BCR-ABL protein encoded by the BCR-ABL C2506TmRNA may comprise a sequence of at least 75%, at least 80%, at least85%, at least 90%, at least 95%, at least 99%, or identical to least 20contiguous amino acids of SEQ ID NO: 19.

In some examples, CML patients undergoing kinase inhibitor therapy maydevelop two kinds of mutations: a) an truncation mutant of BCR-ABLprotein such as Del 2595-2779, Del 2596-2597, 2417insCAGG, C2506T and b)one or more point mutations in the kinase domain of Abl. Exemplary pointmutations in the Abl kinase domain include: Q252H, G250E, H396R, F359V,M244V, E255K, Y253H, E255V, T315I (Position numberings of these mutantsare based on the wild type ABL protein, GenBank accession numberAAA51561).

In some examples, the truncation variant of BCR-ABL mRNA can be detectedsimultaneously with the detection of mutations in ABL portion of BCR-ABLmRNA. In another example, the mutations in the ABL portion of BCR-ABLmRNA can be detected separately. Several methods are known in the artfor detection of the presence or absence of such mutations. Non limitingexamples include, DNA sequencing, detection by hybridization of adetectably labeled probe, detection by size, allele specific PCR,ligation amplification reaction (LAR), detection by oligonucleotidearrays.

Biological Sample Collection and Preparation

The methods provided herein may be performed using any biologicalsample. Biological samples may be obtained by standard procedures andmay be used immediately or stored (e.g., the sample may be frozenbetween about −15° C. to about −100° C.) for later use. The presence ofnucleic acids having BCR-ABL truncation mutation in a sample can bedetermined by amplifying all portions of BCR-ABL nucleic acid. Thus, anyliquid or solid material believed to contain BCR-ABL nucleic acids canbe an appropriate sample. Preferred the sample is blood. More preferablythe sample is plasma. In one example, the sample may be obtained from anindividual who is suspected of having a disease, or a geneticabnormality. In another example sample may be obtained from a healthyindividual who is assumed of having no disease, or a geneticabnormality. In preferred examples, the sample may be obtained frommyeloproliferative disease patients undergoing kinase inhibitor therapy.In another example, sample may be obtained from myeloproliferativedisease patients not undergoing kinase inhibitor therapy.

In another example, nucleic acid may be mRNA or cDNA generated from mRNAor total RNA may be used. RNA is isolated from cells or tissue samplesusing standard techniques, see, e.g., Sambrook, et al., MolecularCloning: A Laboratory Manual, Second Edition (1989), Cold Spring HarborPress, Plainview, N.Y. In addition, reagents and kits for isolating RNAfrom any biological sample such as whole blood, plasma, serum, buffycoat, bone marrow, other body fluids, lymphocytes, cultured cells,tissue, and forensic specimens are commercially available e.g., RNeasyProtect Mini kit, RNeasy Protect Cell Mini kit, QIAamp RNA Blood Minikit, RNeasy Protect Saliva Mini kit, Paxgene Blood RNA kit from Qiagen;MELT™, RNaqueous®, ToTALLY RNA™, RiboPure™-Blood, Poly(A)Purist™ fromApplied Biosystems; TRIZOL® reagent, Dynabeads® mRNA direct kit fromInvitrogen.

Nucleic Acid Amplification

Nucleic acids may be amplified by various methods known to the skilledartisan. Nucleic acid amplification may be linear or exponential.Amplification is generally carried out using polymerase chain reaction(PCR) technologies known in the art. See e.g., Mullis and Faloona,Methods Enzymol. (1987), 155:335, U.S. Pat. Nos. 4,683,202, 4,683,195and 4,800,159.

Alternative methods to PCR include for example, isothermal amplificationmethods, rolling circle methods, Hot-start PCR, real-time PCR,Allele-specific PCR, Assembly PCR or Polymerase Cycling Assembly (PCA),Asymmetric PCR, Colony PCR, Emulsion PCR, Fast PCR, Real-Time PCR,nucleic acid ligation, Gap Ligation Chain Reaction (Gap LCR),Ligation-mediated PCR, Multiplex Ligation-dependent Probe Amplification,(MLPA), Gap Extension Ligation PCR (GEXL-PCR), quantitative PCR (Q-PCR),Quantitative real-time PCR (QRT-PCR), multiplex PCR, Helicase-dependentamplification, Intersequence-specific (ISSR) PCR, Inverse PCR,Linear-After-The-Exponential-PCR (LATE-PCR), Methylation-specific PCR(MSP), Nested PCR, Overlap-extension PCR, PAN-AC assay, ReverseTranscription PCR (RT-PCR), Rapid Amplification of cDNA Ends (RACE PCR),Single molecule amplification PCR (SMA PCR), Thermal asymmetricinterlaced PCR (TAIL-PCR), Touchdown PCR, long PCR, nucleic acidsequencing (including DNA sequencing and RNA sequencing), transcription,reverse transcription, duplication, DNA or RNA ligation, and othernucleic acid extension reactions known in the art. The skilled artisanwill understand that other methods may be used either in place of, ortogether with, PCR methods, including enzymatic replication reactionsdeveloped in the future. See, e.g., Saiki, “Amplification of GenomicDNA” in PCR Protocols, Innis et al., eds., Academic Press, San Diego,Calif., 13-20 (1990); Wharam, et al., 29(11) Nucleic Acids Res, E54-E54(2001); Hafner, et al., 30(4) Biotechniques, 852-6, 858, 860 passim(2001).

Nucleic Acid Detection

Amplification of nucleic acids can be detected by any of a number ofmethods well-known in the art such as gel electrophoresis, columnchromatography, hybridization with a probe, or sequencing.

Detectable labels can be used to identify the probe hybridized to agenomic nucleic acid or reference nucleic acid. Detectable labelsinclude but are not limited to fluorophores, isotopes (e.g., ³²P, ³³P,³⁵S, ³H, ¹⁴C, ¹²⁵I, ¹³¹I) electron-dense reagents (e.g., gold, silver),nanoparticles, enzymes commonly used in an ELISA (e.g., horseradishperoxidase, beta-galactosidase, luciferase, alkaline phosphatase),chemiluminiscent compound, colorimetric labels (e.g., colloidal gold),magnetic labels (e.g., Dynabeads™), biotin, digoxigenin, haptens,proteins for which antisera or monoclonal antibodies are available,ligands, hormones, oligonucleotides capable of forming a complex withthe corresponding oligonucleotide complement.

One general method for real time PCR uses fluorescent probes such as theTaqMan® probes (Heid, et al., Genome Res 6: 986-994, 1996), molecularbeacons, and Scorpions™. Real-time PCR quantifies the initial amount ofthe template with more specificity, sensitivity and reproducibility,than other forms of quantitative PCR, which detect the amount of finalamplified product. Real-time PCR does not detect the size of theamplicon. The probes employed in Scorpion™ and TaqMan® technologies arebased on the principle of fluorescence quenching and involve a donorfluorophore and a quenching moiety.

In a preferred example, the detectable label is a fluorophore. The term“fluorophore” as used herein refers to a molecule that absorbs light ata particular wavelength (excitation frequency) and subsequently emitslight of a longer wavelength (emission frequency). The term “donorfluorophore” as used herein means a fluorophore that, when in closeproximity to a quencher moiety, donates or transfers emission energy tothe quencher. As a result of donating energy to the quencher moiety, thedonor fluorophore will itself emit less light at a particular emissionfrequency that it would have in the absence of a closely positionedquencher moiety.

The term “quencher moiety” as used herein means a molecule that, inclose proximity to a donor fluorophore, takes up emission energygenerated by the donor and either dissipates the energy as heat or emitslight of a longer wavelength than the emission wavelength of the donor.In the latter case, the quencher is considered to be an acceptorfluorophore. The quenching moiety can act via proximal (i.e.,collisional) quenching or by Förster or fluorescence resonance energytransfer (“FRET”). Quenching by FRET is generally used in TaqMan® probeswhile proximal quenching is used in molecular beacon and Scorpion™ typeprobes.

Suitable fluorescent moieties include but are not limited to thefollowing fluorophores working individually or in combination:

4-acetamido-4′-isothiocyanatostilbene-2,2′disulfonic acid; acridine andderivatives: acridine, acridine isothiocyanate; Alexa Fluors: AlexaFluor® 350, Alexa Fluor® 488, Alexa Fluor® 546, Alexa Fluor® 555, AlexaFluor® 568, Alexa Fluor® 594, Alexa Fluor® 647 (Molecular Probes);5-(2′-aminoethyl)aminonaphthalene-1-sulfonic acid (EDANS);4-amino-N-[3-vinylsulfonyl)phenyl]naphthalimide-3,5 disulfonate (LuciferYellow VS); N-(4-anilino-1-naphthyl)maleimide; anthranilamide; BlackHole Quencher™ (BHQ™) dyes (biosearch Technologies); BODIPY dyes:BODIPY® R-6G, BOPIPY® 530/550, BODIPY® FL; Brilliant Yellow; coumarinand derivatives: coumarin, 7-amino-4-methylcoumarin (AMC, Coumarin 120),7-amino-4-trifluoromethylcouluarin (Coumarin 151); Cy2®, Cy3®, Cy3.5®,Cy5®, Cy5.5®; cyanosine; 4′,6-diaminidino-2-phenylindole (DAPI); 5′,5″-dibromopyrogallol-sulfonephthalein (Bromopyrogallol Red);7-diethylamino-3-(4′-isothiocyanatophenyl)-4-methylcoumarin;diethylenetriamine pentaacetate;4,4′-diisothiocyanatodihydro-stilbene-2,2′-disulfonic acid;4,4′-diisothiocyanatostilbene-2,2′-disulfonic acid;5-[dimethylamino]naphthalene-1-sulfonyl chloride (DNS, dansyl chloride);4-(4′-dimethylaminophenylazo)benzoic acid (DABCYL);4-dimethylaminophenylazophenyl-4′-isothiocyanate (DABITC); Eclipse™(Epoch Biosciences Inc.); eosin and derivatives: eosin, eosinisothiocyanate; erythrosin and derivatives: erythrosin B, erythrosinisothiocyanate; ethidium; fluorescein and derivatives:5-carboxyfluorescein (FAM), 5-(4,6-dichlorotriazin-2-yl)aminofluorescein(DTAF), 2′,7′-dimethoxy-4′5′-dichloro-6-carboxyfluorescein (JOE),fluorescein, fluorescein isothiocyanate (FITC),hexachloro-6-carboxyfluorescein (HEX), QFITC (XRITC),tetrachlorofluorescein (TET); fluorescamine; IR144; IR1446; lanthamidephosphors; Malachite Green isothiocyanate; 4-methylumbelliferone; orthocresolphthalein; nitrotyrosine; pararosaniline; Phenol Red;B-phycoerythrin, R-phycoerythrin; allophycocyanin; o-phthaldialdehyde;Oregon Green®; propidium iodide; pyrene and derivatives: pyrene, pyrenebutyrate, succinimidyl 1-pyrene butyrate; QSY® 7; QSY® 9; QSY® 21; QSY®35 (Molecular Probes); Reactive Red 4 (Cibacron® Brilliant Red 3B-A);rhodamine and derivatives: 6-carboxy-X-rhodamine (ROX),6-carboxyrhodamine (R6G), lissamine rhodamine B sulfonyl chloride,rhodamine (Rhod), rhodamine B, rhodamine 123, rhodamine green, rhodamineX isothiocyanate, riboflavin, rosolic acid, sulforhodamine B,sulforhodamine 101, sulfonyl chloride derivative of sulforhodamine 101(Texas Red); terbium chelate derivatives;N,N,N′,N′-tetramethyl-6-carboxyrhodamine (TAMRA); tetramethyl rhodamine;tetramethyl rhodamine isothiocyanate (TRITC).

Other fluorescent nucleotide analogs can be used, see, e.g., Jameson,Meth. Enzymol. (1997), 278:363-390; Zhu et al., Nucleic Acids Res.(1994), 22:3418-3422. U.S. Pat. Nos. 5,652,099 and 6,268,132 alsodescribe nucleoside analogs for incorporation into nucleic acids, e.g.,DNA and/or RNA, or oligonucleotides, via either enzymatic or chemicalsynthesis to produce fluorescent oligonucleotides. U.S. Pat. No.5,135,717 describes phthalocyanine and tetrabenztriazaporphyrin reagentsfor use as fluorescent labels.

The detectable label can be incorporated into, associated with orconjugated to a nucleic acid. Label can be attached by spacer arms ofvarious lengths to reduce potential steric hindrance or impact on otheruseful or desired properties. See, e.g., Mansfield, Mol. Cell. Probes(1995), 9:145-156.

Detectable labels can be incorporated into nucleic acid probes bycovalent or non-covalent means, e.g., by transcription, such as byrandom-primer labeling using Klenow polymerase, or nick translation, or,amplification, or equivalent as is known in the art. For example, anucleotide base is conjugated to a detectable moiety, such as afluorescent dye, e.g., Cy3™ or Cy5™ and then incorporated into nucleicacid probes during nucleic acid synthesis or amplification. Nucleic acidprobes can thereby be labeled when synthesized using Cy3™- or Cy5™-dCTPconjugates mixed with unlabeled dCTP.

Nucleic acid probes can be labeled by using PCR or nick translation inthe presence of labeled precursor nucleotides, for example, modifiednucleotides synthesized by coupling allylamine-dUTP to thesuccinimidyl-ester derivatives of the fluorescent dyes or haptens (suchas biotin or digoxigenin) can be used; this method allows custompreparation of most common fluorescent nucleotides, see, e.g., Henegariuet al., Nat. Biotechnol. (2000), 18:345-348,

Nucleic acid probes may be labeled by non-covalent means known in theart. For example, Kreatech Biotechnology's Universal Linkage System®(ULS®) provides a non-enzymatic labeling technology, wherein a platinumgroup forms a co-ordinative bond with DNA, RNA or nucleotides by bindingto the N7 position of guanosine. This technology may also be used tolabel proteins by binding to nitrogen and sulfur containing side chainsof amino acids. See, e.g., U.S. Pat. Nos. 5,580,990; 5,714,327; and5,985,566; and European Patent No. EP 0539466.

Labeling with a detectable label also can include a nucleic acidattached to another biological molecule, such as a nucleic acid, e.g.,an oligonucleotide, or a nucleic acid in the form of a stem-loopstructure as a “molecular beacon” or an “aptamer beacon”. Molecularbeacons as detectable moieties are well known in the art; for example,Sokol (Proc. Natl. Acad. Sci. USA (1998), 95:11538-11543) synthesized“molecular beacon” reporter oligodeoxynucleotides with matchedfluorescent donor and acceptor chromophores on their 5′ and 3′ ends. Inthe absence of a complementary nucleic acid strand, the molecular beaconremains in a stem-loop conformation where fluorescence resonance energytransfer prevents signal emission. On hybridization with a complementarysequence, the stem-loop structure opens increasing the physical distancebetween the donor and acceptor moieties thereby reducing fluorescenceresonance energy transfer and allowing a detectable signal to be emittedwhen the beacon is excited by light of the appropriate wavelength. Seealso, e.g., Antony (Biochemistry (2001), 40:9387-9395,), describing amolecular beacon consist of a G-rich 18-mer triplex formingoligodeoxyribonucleotide. See also U.S. Pat. Nos. 6,277,581 and6,235,504.

Aptamer beacons are similar to molecular beacons; see, e.g., Hamaguchi,Anal. Biochem. (2001), 294:126-131; Poddar, Mol. Cell. Probes (2001),15:161-167; Kaboev, Nucleic Acids Res. (2000), 28:E94. Aptamer beaconscan adopt two or more conformations, one of which allows ligand binding.A fluorescence-quenching pair is used to report changes in conformationinduced by ligand binding. See also, e.g., Yamamoto et al., Genes Cells(2000), 5:389-396; Smimov et al., Biochemistry (2000), 39:1462-1468.

The nucleic acid probe may be indirectly detectably labeled via apeptide. A peptide can be made detectable by incorporating predeterminedpolypeptide epitopes recognized by a secondary reporter (e.g., leucinezipper pair sequences, binding sites for secondary antibodies,transcriptional activator polypeptide, metal binding domains, epitopetags). A label may also be attached via a second peptide that interactswith the first peptide (e.g., S-S association).

As readily recognized by one of skill in the art, detection of thecomplex containing the nucleic acid from a sample hybridized to alabeled probe can be achieved through use of a labeled antibody againstthe label of the probe. In a preferred example, the probe is labeledwith digoxigenin and is detected with a fluorescent labeledanti-digoxigenin antibody. In another example, the probe is labeled withFITC, and detected with fluorescent labeled anti-FITC antibody. Theseantibodies are readily available commercially. In another example, theprobe is labeled with FITC, and detected with anti-FITC antibody primaryantibody and a labeled anti-anti FITC secondary antibody.

Detection of Nucleic Acid by Size:

Methods for detecting the presence or amount of nucleic acid are wellknown in the art and any of them can be used in the methods describedherein so long as they are capable of separating individual nucleic acidby the difference in size of the amplicons. The separation techniqueused should permit resolution of nucleic acid as long as they differfrom one another by at least one nucleotide. The separation can beperformed under denaturing or under non-denaturing or nativeconditions—i.e., separation can be performed on single- ordouble-stranded nucleic acids. It is preferred that the separation anddetection permits detection of length differences as small as onenucleotide. It is further preferred that the separation and detectioncan be done in a high-throughput format that permits real time orcontemporaneous determination of amplicon abundance in a plurality ofreaction aliquots taken during the cycling reaction. Useful methods forthe separation and analysis of the amplified products include, but arenot limited to, electrophoresis (e.g., agarose gel electrophoresis,capillary electrophoresis (CE)), chromatography (HPLC), and massspectrometry.

DNA Sequencing:

In some examples, detection of nucleic acid is by DNA sequencing.Sequencing may be carried out by the dideoxy chain termination method ofSanger et al. (Proceedings of the National Academy of Sciences USA(1977), 74, 5463-5467) with modifications by Zimmermann et al. (NucleicAcids Res. (1990), 18:1067). Sequencing by dideoxy chain terminationmethod can be performed using Thermo Sequenase (Amersham Pharmacia,Piscataway, N.J.), Sequenase reagents from US Biochemicals or Sequathermsequencing kit (Epicenter Technologies, Madison, Wis.). Sequencing mayalso be carried out by the “RR dRhodamine Terminator Cycle SequencingKit” from PE Applied Biosystems (product no. 403044, Weiterstadt,Germany), Taq DyeDeoxy™ Terminator Cycle Sequencing kit and method(Perkin-Elmer/Applied Biosystems) in two directions using an AppliedBiosystems Model 373A DNA or in the presence of dye terminators CEQ™ DyeTerminator Cycle Sequencing Kit, (Beckman 608000). Alternatively,sequencing can be performed by a method known as Pyrosequencing(Pyrosequencing, Westborough, Mass.). Detailed protocols forPyrosequencing can be found in: Alderborn et al., Genome Res. (2000),10:1249-1265.

Detection of BCR-ABL Truncation Mutation by Hybridization of a NucleicAcid Probe

BCR-ABL truncation mutation may be detected by hybridization of anucleic acid probe to genomic DNA or to a portion of amplified nucleicacid comprising the mutation. Probes may encompass the deletion junction(for Del 2595-2779: nucleotides 2594 and 2595 of SEQ ID NO: 3; for del2596-2597: nucleotides 2595 and 2596 of SEQ ID NO: 7; for 2417insCAGG:nucleotides 2418-2421 of SEQ ID NO: 12) or mutation site (nucleotideposition 2506 of SEQ ID NO: 17) of BCR-ABL nucleic acid where a firstportion of the probe may be specific for a portion of BCR-ABL nucleicacid in the 5′-end of the deletion junction or mutation site and asecond portion of the probe may be specific 3′-end of the deletionjunction or mutation site.

Cloning

The nucleic acid (e.g., cDNA or genomic DNA) encoding at least a portionof BCR-ABL or its variants may be inserted into a replicable vector forcloning (amplification of the DNA) or for expression. Various vectorsare publicly available. The vector may, for example, be in the form of aplasmid, cosmid, viral particle, or phage. The appropriate nucleic acidsequence may be inserted into the vector by a variety of procedures. Ingeneral, DNA is inserted into an appropriate restriction endonucleasesite(s) using techniques known in the art, see Sambrook, et al.,Molecular Cloning: A Laboratory Manual (1989), Second Edition, ColdSpring Harbor Press, Plainview, N.Y.

Prokaryotic Vectors:

Prokaryotic transformation vectors are well-known in the art and includepBlueskript and phage Lambda ZAP vectors (Stratagene, La Jolla, Calif.),and the like. Other suitable vectors and promoters are disclosed indetail in U.S. Pat. No. 4,798,885, issued Jan. 17, 1989, the disclosureof which is incorporated herein by reference in its entirety.

Other suitable vectors for transformation of E. coli cells include thepET expression vectors (Novagen, see U.S. Pat. No. 4,952,496), e.g.,pET11a, which contains the T7 promoter, T7 terminator, the inducible E.coli lac operator, and the lac repressor gene; and pET 12a-c, whichcontain the T7 promoter, T7 terminator, and the E. coli ompT secretionsignal. Another suitable vector is the pIN-IIIompA2 (see Duffaud et al.,Meth. in Enzymology, 153:492-507, 1987), which contains the lpppromoter, the lacUV5 promoter operator, the ompA secretion signal, andthe lac repressor gene.

Eukaryotic Vectors:

Exemplary, eukaryotic transformation vectors, include the cloned bovinepapilloma virus genome, the cloned genomes of the murine retroviruses,and eukaryotic cassettes, such as the pSV-2 gpt system [described byMulligan and Berg, Nature Vol. 277:108-114 (1979)] the Okayama-Bergcloning system [Mol. Cell. Biol. Vol. 2:161-170 (1982)], and theexpression cloning vector described by Genetics Institute (Science.1985; 228: 810-815), pCMV Sport, pCDNA™ 3.3 TOPO®, BaculoDirect™Baculovirus Expression System (Invitrogen Corp., Carlsbad, Calif., USA),StrataClone™ (Stratagene, CA, USA), pBAC vectors (EMD Chemicals Inc, NJ,USA).

Vector Components:

Vector components generally include, but are not limited to, one or moreof a regulatory elements such as an enhancer element, a promoter, and atranscription termination sequence, an origin of replication, one ormore selection marker genes, and a cloning site.

Vectors encoding BCR-ABL nucleic acid sequence and its variants mayfurther comprise non-BCR-ABL nucleic acid sequence which may beco-expressed with BCR-ABL and its variants either as a fusion product oras a co-transcript. Non limiting examples of such non-BCR-ABL nucleicacid sequence include His-tag (a stretch of poly histidines), FLAG-tag,and Green Fluorescent Protein (GFP). His-tag and FLAG-tag can be used toin many different methods, such as purification of BCR-ABL protein andor truncation mutant of BCR-ABL protein fused to such tags. The tags canalso serve as an important site for antibody recognition. This isparticularly important in detecting BCR-ABL proteins and or truncationmutant of BCR-ABL protein fused to such tags. GFP may be used as areporter of expression (Phillips G. J. FEMS Microbiol. Lett. 2001; 204(1): 9-18), such as the expression of BCR-ABL and the truncation variantof BCR-ABL. Exemplary design of vectors encoding BCR-ABL and thetruncation variant of BCR-ABL sequence is shown in FIGS. 3A and 3Brespectively.

Expression vectors used in eukaryotic host cells (yeast, fungi, insect,plant, animal, human, or nucleated cells from other multicellularorganisms) will also contain sequences necessary for the termination oftranscription and for stabilizing the mRNA. Such sequences are commonlyavailable from the 5′ and, occasionally 3′, untranslated regions ofeukaryotic or viral DNA or cDNA. These regions contain nucleotidesegments transcribed as polyadenylated fragments in the untranslatedportion of the mRNA encoding BCR-ABL.

Still other methods, vectors, and host cells suitable for adaptation tothe synthesis of BCR-ABL in recombinant vertebrate cell culture aredescribed in Gething et al., Nature (1981), 293:620-625; Mantei et al.,Nature. 1979; 281:40-46; EP 117,060; and EP 117,058.

Genetically Modifying Host Cells by Introducing Recombinant Nucleic Acid

The recombinant nucleic acid (e.g., cDNA or genomic DNA) encoding atleast a portion of BCR-ABL or its variants may be introduced into hostcells thereby genetically modifying the host cell. Host cells may beused for cloning and/or for expression of the recombinant nucleic acid.Host cells can be prokaryotic, for example bacteria. Host cell can bealso be eukaryotic which includes but not limited to yeast, fungal cell,insect cell, plant cell and animal cell. In preferred example, the hostcell can be a mammalian cell. In another preferred example host cell canbe human cell. In one preferred example, the eukaryotic host cell may beK562 cell. K562 cells were the first human immortalized myelogenousleukemia line to be established and are a BCR-ABL positiveerythroleukemia line derived from a CIVIL patient in blast crisis(Lozzio & Lozzio, Blood. 1975; 45(3): 321-334; Drexler, H. G. TheLeukemia-Lymphoma Cell Line Factsbook. (2000), Academic Press.

Host cells may comprise wild-type genetic information. The geneticinformation of the host cells may be altered on purpose to allow it tobe a permissive host for the recombinant DNA. Examples of suchalterations include mutations, partial or total deletion of certaingenes, or introduction of non-host nucleic acid into host cell. Hostcells may also comprise mutations which are not introduced on purpose.

Several methods are known in the art to introduce recombinant DNA inbacterial cells that include but are not limited to transformation,transduction, and electroporation, see Sambrook, et al., MolecularCloning: A Laboratory Manual (1989), Second Edition, Cold Spring HarborPress, Plainview, N.Y. Non limiting examples of commercial kits andbacterial host cells for transformation include NovaBlue Singles™ (EMDChemicals Inc, NJ, USA), Max Efficiency® DH5α™, One Shot® BL21 (DE3) E.coli cells, One Shot® BL21 (DE3) pLys E. coli cells (Invitrogen Corp.,Carlsbad, Calif., USA), XL1-Blue competent cells (Stratagene, CA, USA).Non limiting examples of commercial kits and bacterial host cells forelectroporation include Zappers™ electrocompetent cells (EMD ChemicalsInc, NJ, USA), XL1-Blue Electroporation-competent cells (Stratagene, CA,USA), ElectroMAX™ A. tumefaciens LBA4404 Cells (Invitrogen Corp.,Carlsbad, Calif., USA).

Several methods are known in the art to introduce recombinant nucleicacid in eukaryotic cells. Exemplary methods include transfection,electroporation, liposome mediated delivery of nucleic acid,microinjection into to the host cell, see Sambrook, et al., MolecularCloning: A Laboratory Manual (1989), Second Edition, Cold Spring HarborPress, Plainview, N.Y. Non limiting examples of commercial kits andreagents for transfection of recombinant nucleic acid to eukaryotic cellinclude Lipofectamine™ 2000, Optifect™ Reagent, Calcium PhosphateTransfection Kit (Invitrogen Corp., Carlsbad, Calif., USA), GeneJammer®Transfection Reagent, LipoTAXI® Trasfection Reagent (Stratagene, CA,USA). Alternatively, recombinant nucleic acid may be introduced intoinsect cells (e.g. sf9, sf21, High Five™) by using baculo viral vectors.

In one preferred example, an exemplary vector comprising the cDNAsequence of BCR-ABL truncation variant (pCMV/GFP/truncation mutantBCR-ABL, shown in FIG. 2B) may be transfected into K562 cells. Stabletransfected K 562 cells may be developed by transfecting the cells withvarying amounts of the pCMV/GFP/truncation mutant vector (0 ng-500 ng)using various methods known in the art. In one exemplary method, TheProFection® Mammalian Transfection System—Calcium Phosphate (PromegaCorporation, WI, USA) may be used. This is a simple system containingtwo buffers: CaCl2 and HEPES-buffered saline. A precipitate containingcalcium phosphate and DNA is formed by slowly mixing a HEPES-bufferedphosphate solution with a solution containing calcium chloride and DNA.These DNA precipitates are then distributed onto eukaryotic cells andenter the cells through an endocytic-type mechanism. This transfectionmethod has been successfully used by others (Hay et al. J. Biol. Chem.2004; 279: 1650-58). The transfected K562 cells can be selected from thenon-transfected cells by using the antibiotics Neomycin and Ampicillin.Expression of the truncation variant of BCR-ABL can assessed from theco-expression of the reporter gene GFP.

Alternatively, in a 24-well format complexes are prepared using a DNA(μg) to Lipofectamine™ 2000 (Invitrogen Corporation, Carlsbad, Calif.,USA) (pi) ratio of 1:2 to 1:3. Cells are transfected at high celldensity for high efficiency, high expression levels, and to minimizecytotoxicity. Prior to preparing complexes, 4-8×10⁵ cells are plated in500 μl of growth medium without antibiotics. For each transfectionsample, complexes are prepared as follows: a. DNA is diluted in 50 μl ofOpti-MEM® I Reduced Serum Medium without serum (Invitrogen Corporation,Carlsbad, Calif., USA) or other medium without serum and mixed gently.b. Lipofectamine™ 2000 is mixed gently before use and the mixture isdiluted to appropriate amount in 50 μl of Opti-MEM® I Medium. Themixture is incubated for 5 minutes at room temperature. c. After 5minute incubation, the diluted DNA is combined with dilutedLipofectamine™ 2000 (total volume=100 μl) and is mixed gently. Themixture is incubated for 20 minutes at room temperature. 100 μl ofcomplexes is added to each well containing cells and medium. Thecontents are mixed gently by rocking the plate back and forth. Cells areincubated at 37° C. in a CO2 incubator for 18-48 hours prior to testingfor transgene expression. Medium may be changed after 4-6 hours. Cellsare passaged at a 1:10 (or higher dilution) into fresh growth medium 24hours after transfection. Selective medium (containing Neomycin andAmpicillin) is added the following day.

Isolation of BCR-ABL Polypeptide

BCR-ABL proteins with and without truncation mutation may be recoveredfrom biological sample from an individual, culture medium or from hostcell lysates. If membrane-bound, it can be released from the membraneusing a suitable detergent solution (e.g., Triton-X 100) or by enzymaticcleavage. Cells employed in the expression of BCR-ABL protein can bedisrupted by various physical or chemical means, such as freeze-thawcycling, sonication, mechanical disruption, or cell lysing agents.

It may be desired to purify BCR-ABL protein from recombinant cellproteins or polypeptides. The following procedures are exemplary ofsuitable purification procedures: by fractionation on an ion-exchangecolumn; ethanol precipitation; reverse phase HPLC; chromatography onsilica or on a cation-exchange resin such as DEAE; chromatofocusing;SDS-PAGE; ammonium sulfate precipitation; gel filtration using, forexample, Sephadex G-75; protein A Sepharose columns to removecontaminants such as IgG; and metal chelating columns to bindepitope-tagged forms of the BCR-ABL. Various methods of proteinpurification may be employed and such methods are known in the art anddescribed for example in Deutscher, Methods in Enzymology (1990),182:83-89; Scopes, Protein Purification: Principles and Practice,Springer-Verlag, New York (1982). The purification step(s) selected willdepend, for example, on the nature of the production process, source ofBCR-ABL used and the particular BCR-ABL produced.

Detection of BCR-ABL Polypeptide

Several methods for detection of proteins are well known in the art.Detection of the proteins could be by resolution of the proteins by SDSpolyacrylamide gel electrophoresis (SDS PAGE), followed by staining theproteins with suitable stain for example, Coomassie Blue. The BCR-ABLproteins with and without the truncation mutation can be differentiatedfrom each other and also from other proteins based on their molecularweight and migration on SDS PAGE. BCR-ABL proteins with and without thetruncation mutation can be differentiated from each other and from otherproteins and also can be identified by Western blot analysis. Methods ofWestern blot are well known in the art and described for example in W.Burnette W. N. Anal. Biochem. 1981; 112 (2): 195-203. Briefly, BCR-ABLproteins can be subjected to SDS PAGE. Following the gelelectrophoresis, the proteins can be transferred on nitrocellulose orpolyvinylidene fluoride (PVDF) membrane. The membranes are blocked withsuitable blocking agents to prevent non-specific binding of antibody tothe membrane. Suitable blocking agents include bovine serum albumin,non-fat dry milk. After blocking and several washes with suitablebuffer, antibodies that specifically bind to the BCR-ABL protein withoutany truncation mutation and antibodies that specifically bind to BCR-ABLprotein with truncation mutation are allowed to bind to the protein ofinterest. Following the binding of primary antibody to the protein ofinterest, the excess antibodies are washed away with suitable buffer. Asuitable secondary antibody that is able to bind to the primary antibodyis applied. The secondary antibody is detectably labeled. Excesssecondary antibody is washed away with suitable buffer and thedetectable label of the secondary antibody is detected. Detection of thedetectable label of the secondary antibody indicates the presence of theprotein of interest. If primary antibodies specific for the truncationmutant of BCR-ABL protein is used, then the truncation mutant of BCR-ABLprotein can be identified.

In preferred examples, Flow Cytometry may be applied to detect thetruncation mutant of BCR-ABL protein with or without truncationmutation. Antibodies specific for the wild-type or truncation mutant ofBCR-ABL protein can be coupled to beads and can be used in the FlowCytometry analysis.

In some examples, protein microarrays may be applied to identifytruncation mutant of BCR-ABL protein and can be used to differentiatefrom BCR-ABL protein without such mutation. Methods of protein arraysare well known in the art. In one example, antibodies specific for eachprotein may be immobilized on the solid surface such as glass or nylonmembrane. The proteins can then be immobilized on the solid surfacethrough the binding of the specific antibodies. Antibodies may beapplied that bind specifically to a second epitope of the BCR-ABLproteins with and without truncation mutation. The firstantibody/protein/second antibody complex can then be detected using adetectably labeled secondary antibody. The detectable label can bedetected as discussed for nucleic acid.

Antibody Production and Screening

Various procedures known in the art may be used for the production ofantibodies to epitopes of the BCR-ABL protein and the truncation mutantsof BCR-ABL protein. Such antibodies include but are not limited topolyclonal, monoclonal, chimeric, single chain, Fab fragments andfragments produced by a Fab expression library. Antibodies thatspecifically bind to an epitope of SEQ ID NO's: 6, 10, 15, or 19 areuseful for detection and diagnostic purposes.

In one examples, the antibodies may bind specifically to an epitopecomprising at least 10 contiguous amino acids of SEQ ID NO: 20, 11, 16.Such antibodies are useful for detection and diagnostic purposes.

Monoclonal antibodies that bind BCR-ABL protein and the truncationmutants of BCR-ABL protein may be radioactively labeled allowing one tofollow their location and distribution in the body after injection.Radioactivity tagged antibodies may be used as a non-invasive diagnostictool for imaging de novo cells of tumors and metastases.

Immunotoxins may also be designed which target cytotoxic agents tospecific sites in the body. For example, specific monoclonal antibodieswith high affinity for BCR-ABL protein and truncation mutants of BCR-ABLprotein may be covalently complexed to bacterial or plant toxins, suchas diphtheria toxin, abrin or ricin. A general method of preparation ofantibody/hybrid molecules may involve use of thiol-crosslinking reagentssuch as SPDP, which attack the primary amino groups on the antibody andby disulfide exchange, attach the toxin to the antibody. The hybridantibodies may be used to specifically eliminate BCR-ABL protein andtruncation mutants of BCR-ABL protein expressing cells.

For the production of antibodies, various host animals may be immunizedby injection with the full length or fragment of BCR-ABL protein and thetruncation mutants of BCR-ABL protein including but not limited torabbits, mice, rats, etc. Various adjuvants may be used to increase theimmunological response, depending on the host species, including but notlimited to Freund's (complete and incomplete), mineral gels such asaluminum hydroxide, surface active substances such as lysolecithin,pluronic polyols, polyanions, peptides, oil emulsions, keyhole limpethemocyanin, dinitrophenol, and potentially useful human adjuvants suchas BCG (bacilli Calmette-Guerin) and Corynebacterium parvum.

Monoclonal antibodies to BCR-ABL protein and the truncation mutant ofBCR-ABL protein may be prepared by using any technique which providesfor the production of antibody molecules by continuous cell lines inculture. These include but are not limited to the hybridoma techniqueoriginally described by Kohler and Milstein, (Nature (1975),256:495-497), the human B-cell hybridoma technique (Kosbor et al.,Immunology Today (1983), 4:72; Cote et al. Proc. Natl. Acad. Sci.(1983), 80:2026-2030) and the EBV-hybridoma technique (Cole et al.,Monoclonal Antibodies and Cancer Therapy (1985), Alan R. Liss, Inc., pp.77-96). In addition, techniques developed for the production of“chimeric antibodies” (Morrison et al., Proc. Natl. Acad. Sci. USA(1984), 81:6851-6855; Neuberger et al., Nature (1984), 312:604-608;Takeda et al., Nature (1985), 314:452-454) by splicing the genes from amouse antibody molecule of appropriate antigen specificity together withgenes from a human antibody molecule of appropriate biological activitycan be used. Alternatively, techniques described for the production ofsingle chain antibodies (U.S. Pat. No. 4,946,778) can be adapted toproduce BCR-ABL protein and truncation mutant of BCR-ABLprotein-specific single chain antibodies.

Antibody fragments which contain specific binding sites of BCR-ABLprotein and truncation mutants of BCR-ABL protein may be generated byknown techniques. For example, such fragments include but are notlimited to: the F(ab′)₂ fragments which can be produced by pepsindigestion of the antibody molecule and the Fab fragments which can begenerated by reducing the disulfide bridges of the F(ab′)₂ fragments.Alternatively, Fab expression libraries may be constructed (Huse et al.,Science. 1989; 246: 1275-1281) to allow rapid and easy identification ofmonoclonal Fab fragments with the desired specificity to BCR-ABL proteinand truncation mutant of BCR-ABL protein.

Kits

Kits for diagnostic are provided. A diagnostic system may include a kitwhich contains, in an amount sufficient for at least one assay, any ofthe hybridization assay probes, amplification primers, and/or antibodiesagainst BCR-ABL wild type and truncation mutant in a packaging material.Typically, the kits will also include instructions recorded in atangible form (e.g., contained on paper or an electronic medium) forusing the packaged probes, primers, and/or antibodies in a detectionassay for determining the presence or amount of BCR-ABL variant mRNA orBCR-ABL truncation mutant protein in a test sample.

The various components of the diagnostic systems may be provided in avariety of forms. For example, the required enzymes, the nucleotidetriphosphates, the probes, primers, and/or antibodies may be provided asa lyophilized reagent. These lyophilized reagents may be pre-mixedbefore lyophilization so that when reconstituted they form a completemixture with the proper ratio of each of the components ready for use inthe assay. In addition, the diagnostic systems may contain areconstitution reagent for reconstituting the lyophilized reagents ofthe kit. In preferred kits for amplifying target nucleic acid derivedfrom a CIVIL patients, the enzymes, nucleotide triphosphates andrequired cofactors for the enzymes are provided as a single lyophilizedreagent that, when reconstituted, forms a proper reagent for use in thepresent amplification methods.

In one example, the kit may comprise at least three lyophilizedoligonucleotides: a primer pair to amplify a portion of BCR-ABL mRNAcomprising exons 8 and 9, and a detectably labeled probe capable ofhybridizing to the amplicon generated. In some preferred kits, at leastthree lyophilized oligonucleotides are the primers for amplification ofat least a portion of BCR-ABL mRNA by semi-nested PCR. The primers mayhave sequences of SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 23. orcomplements and fragments thereof respectively. In some preferred kitsat least five lyophilized oligonucleotide reagents may be of providedhaving sequences of SEQ ID NOs: 21-25 or complements and fragmentsthereof. In some examples, SEQ ID NOs: 22-25 may be used for sequencingthe PCR product.

Some preferred kits may further comprise to a solid support foranchoring the nucleic acid of interest on the solid support. The targetnucleic acid may be anchored to the solid support directly or indirectlythrough a capture probe anchored to the solid support and capable ofhybridizing to the nucleic acid of interest. Examples of such solidsupport include but are not limited to beads, microparticles (forexample, gold and other nano particles), microarray, microwells,multiwell plates. The solid surfaces may comprise a first member of abinding pair and the capture probe or the target nucleic acid maycomprise a second member of the binding pair. Binding of the bindingpair members will anchor the capture probe or the target nucleic acid tothe solid surface. Examples of such binding pairs include but are notlimited to biotin/streptavidin, hormone/receptor, ligand/receptor,antigen/antibody.

In other preferred kits, lyophilized antibodies against BCR-ABL wildtype and truncation mutant protein are provided. In some preferred kitsa primary/secondary antibody pair may be provided. Some preferred kitsmay further comprise to a solid support for anchoring the BCR-ABL wildtype and truncation mutant proteins. Such anchoring of the BCR-ABL wildtype and truncation mutant proteins may be through biotin/streptavidin,antigen/antibody interactions.

Typical packaging materials would include solid matrices such as glass,plastic, paper, foil, micro-particles and the like, capable of holdingwithin fixed limits hybridization assay probes, and/or amplificationprimers. Thus, for example, the packaging materials can include glassvials used to contain sub-milligram (e.g., picogram or nanogram)quantities of a contemplated probe, primer, or antibodies or they can bemicrotiter plate wells to which probes, primers, or antibodies have beenoperatively affixed, i.e., linked so as to be capable of participatingin an amplification and/or detection methods.

The instructions will typically indicate the reagents and/orconcentrations of reagents and at least one assay method parameter whichmight be, for example, the relative amounts of reagents to use peramount of sample. In addition, such specifics as maintenance, timeperiods, temperature, and buffer conditions may also be included.

The diagnostic systems contemplate kits having any of the hybridizationassay probes, amplification primers, or antibodies described herein,whether provided individually or in one of the preferred combinationsdescribed above, for use in determining the presence or amount ofBCR-ABL variant mRNA or BCR-ABL truncation mutant protein in a testsample.

Identifying a Compound for Treating CML Patients

In one preferred example, cell lines expressing BCR-ABL (both wild-typeand/or mutant) proteins may be utilized to screen compounds for treatingCML patients. In preferred examples, the compounds may be targetingBCR-ABL protein. In some examples, the compounds may be inhibitor of ABLkinase activity. Non-limiting examples of kinase inhibitors include butnot limited to imatinib, dasatinib, nilotinib, Bosutinib (SKI-606) andAurora kinase inhibitor VX-680. In other examples, the compounds may notbe an inhibitor of ABL kinase activity.

The effect of the compounds on the cells may be assessed. Severalparameters may be assessed for identifying the compounds that may bebeneficial for treatment of CML patients. Non-limiting examples of theparameters that may be assessed includes cell viability, cellproliferation, apoptosis, kinase activity of BCR-ABL protein, additionalmutations in BCR-ABL protein, additional mutation in ABL protein.

In one example, human chronic myeloid leukemia (CML) cell linesexpressing BCR-ABL (both wild-type and/or mutant) proteins may be usedto study the effect of such compounds on their effect on the cells.Non-limiting examples of human chronic myeloid leukemia (CIVIL) celllines include BV173, K562, KCL-22, and KYO-1, LAMA84, EM2, EM3, BV173,AR230, and KU812 (Mahon, F. X., Blood. 2000; 96: 1070-1079; Lerma et al.Mol. Cancer Ther. 2007; 6(2): 655-66).

In other examples, non-CML cells may be transfected with expressionvectors comprising BCR-ABL gene or variants of BCR-ABL gene includingtruncation variants of BCR-ABL gene resulting in genetically modifiedcells comprising the recombinant polynucleotide. Thus, the transfectedcells will be able to express BCR-ABL protein or its variants. Thegenetically modified cells can be used to screen compounds for treatingCML patients.

In yet other examples, CML cell lines, for example BV173, K562, KCL-22,and KYO-1, LAMA84, EM2, EM3, BV173, AR230, and KU812 may be transfectedwith expression vectors comprising variants of BCR-ABL gene (such as,Del 2595-2779, Del 2596-2597, 2417insCAGG, C2506T) resulting ingenetically modified cells comprising the recombinant polynucleotide.The gene product of the variants of BCR-ABL gene, the truncation mutantof BCR-ABL may impart partial or total resistance to ABL kinaseinhibitors to these genetically modified cells. The genetically modifiedcells may be used to screen compounds for treating CML. The compoundsmay be inhibitors of ABL kinase activity or these compounds may haveother mechanism of action.

The CIVIL cell lines and the genetically modified cell lines asdiscussed above may be grown in appropriate growth medium and usingappropriate selective antibiotics. Methods for cell culture is wellknown in the art (Sambrook, et al., Molecular Cloning: A LaboratoryManual (1989), Second Edition, Cold Spring Harbor Press, Plainview,N.Y.). Several growth media for cell culture are commercially available.Non-limiting examples include GIBCO® RPMI Media 1640, Dulbecco'sModified Eagle Medium (DMEM), DMEM: Nutrient Mixture F-12 (DMEM/F12),Minimum Essential Media (Invitrogen Corp., Carlsbad, Calif., USA), RF-10medium. Non-limiting examples of selective antibiotics includeampicillin, neomycin, Geneticin®, Hygromycin B.

In one preferred example, K562 cells (ATCC catalog no: CCL-243) may begenetically modified by transfecting with different amounts of theexpression vector pCMV/GFP comprising the BCR-ABL gene variants (suchas, Del 2595-2779, Del 2596-2597, 2417insCAGG, C2506T). In one example,the amount the expression vector pCMV/GFP comprising the BCR-ABL genevariants used for transfection can be 0 ng, or can be at least about: 1ng, 2 ng, 5 ng, 7.5 ng, 10 ng, 12.5 ng, 15 ng, 20 ng, 25 ng, 30 ng, 40ng, 50 ng, 60 ng, 75 ng, 100 ng, 125 ng, 200 ng, 500 ng, 750 ng, or 1μg. The transefected cells may be grown in RF-10 medium withneomycin/and or ampicillin.

Assessing the Effect of a Compound for Treatment of CML on GeneticallyModified Cells

Several parameters may be assessed for identifying the compounds thatmay be beneficial for treatment of CML patients. Non-limiting examplesof the parameters that may be assessed includes cell viability, cellproliferation, apoptosis, kinase activity of BCR-ABL protein, additionalmutations in BCR-ABL protein, additional mutation in ABL protein.

Cell Viability:

Cells can be plated at a density of 2 to 2.5×10⁵ cells/mL in RF-10 withvarying amounts of the compound or without the compound. Aliquots aretaken out at 24-hour intervals for assessment of cell viability bytryphan blue exclusion.

Alternatively, cell viability can be measured by colorimetric assay suchas MTT assay (Mosman et al. J. Immunol. Meth. 1983; 65: 55-63).Commercial kits for MTT assay are available. For example, CellTiter 96®Non-Radioactive Cell Proliferation Assay (MTT) (Promega Corporation, WI,USA), Vybrant® MTT Cell Proliferation Assay Kit (Invitrogen Corp.,Carlsbad, Calif., USA).

Cell Proliferation:

Proliferation of the genetically modified cells in presence of acompound for treatment of CIVIL patient can be measured in several ways.The proliferation of the cells can be indicative of the effectiveness ofthe compound for CML therapy.

In one such method, cell proliferation assay can performed using MTStetrazolium such as Cell Titer96 Aqueous (Promega corporation, WI, USA),which measures numbers of viable cells. Between 2×10³ and 2×10⁴ cellsare washed twice in RF-10 and plated in quadruplicate intomicrotiter-plate wells in 100 μL RF-10 plus various doses of thecompound. Controls using the same concentrations of compound withoutcells are set up in parallel. Twenty microliters MTS is added to thewells at daily intervals. Two hours after MTS is added, the plates areread in a microplate auto reader (Dynex Technologies, Billingshurst, UK)at 490-nm wavelength. Results are expressed as the mean optical densityfor each dose of the compound. All experiments are repeated at least 3times.

In another method, cell proliferation assay can be performed bymonitoring the incorporation bromo-deoxyuracil (BrdU) into newlysynthesized DNA. Amount of BrdU incorporated into the DNA will beproportional to the amount of DNA synthesis and will be indicative ofthe proliferating cells. In one such method, detectably labeledanti-BrdU antibody can be used to measure the amount of BrdUincorporated into the cells treated with various amounts of thecompound. In one example, the detectable label can be FITC. The amountof signal from FITC-labeled anti-BrdU bound to the DNA can be measuredby Flow Cytometry. Commercially available kits for flow cytometry basedcell proliferation assays are available. Such as, Click-iT® EdU(Invitrogen Corp., Carlsbad, Calif., USA). ELISA based assays formeasuring BrdU incorporation by proliferating cells care commerciallyavailable examples include BrdU Cell Proliferation Assay kit(Calbiochem, EMD Chemicals Inc, NJ, USA).

In another method, proliferation of cells treated with various amountsof the compound can be measured by monitoring the incorporation ofradioactively labeled deoxynucleotides (Sun et al. Cancer Res. 1999; 59:940-946).

Kinase Activity of BCR-ABL:

The effect of a compound on the kinase activity of the BCR-ABL isassessed by monitoring tyrosine phosphorylation profile of the cellularproteins. CrlkL is a substrate of BCR-ABL tyrosine kinase (Ren et al.Genes Dev. 1994; 8(7): 783-95). Genetically modified cells comprisingrecombinant BCR-ABL or variant so of BCR-ABL including the truncationvariant are grown in presence of various amounts of a compound fortreating CIVIL patients. In a preferred example, the compounds are ABLtyrosine kinase inhibitors. Non-limiting examples of kinase inhibitorsinclude imatinib, nilotinib, dasatinib, Bosutinib (SKI-606) and Aurorakinase inhibitor VX-680. Amount of phosphorylated CrkL protein can bemeasured by using detectably labeled anti-phospho CrkL antibody. In oneexample, the detectable label is phycoerythrin. The signal can bedetected by Flow cytometer. Alternatively, the signal can be detected byFluorescent Microtiter plate reader.

Sequencing of the ABL Kinase Domain:

To further investigate the reason for some cells that do not overexpressBCR-ABL but that have higher resistance to a compound that target theATP-binding site of the ABL kinase domain (such as imatinib, nilotinib,dasatinib, and Aurora kinase inhibitor VX-680) than their sensitivecounterparts, the entire kinase domain of K562-sensitive and -resistantcells can be sequenced. Sequencing can be performed using ABI prism 377automated DNA sequencer (PE Applied Biosystems; USA). Sequence analysiscan performed using the GCG version 10 software.

Example 1 Sample Collection

Patients:

Peripheral blood samples were collected from CML patients with orwithout imatinib resistance. Some of imatinib resistant patients werealso resistant to nilotinib and dasatinib. The diagnosis of CIVIL wasestablished based on the examination of bone marrow morphology,cytogenetic, FISH, and molecular studies. The majority of tested sampleswere fresh, but a significant number used cells frozen in freezing mixand stored at −70° C.

Peripheral Blood Samples:

Venous blood (5-8 ml) were collected from patients diagnosed with CMLusing BD Vacutainer™ CPT™ tubes (Beckton Dickenson, NJ, USA, Catalognumber: 362760) by venous puncture. Peripheral mononuclear cells andplatelets were isolated using manufacturer's protocol. Briefly, venousblood collected into the CPT™ tube was mixed with the anticoagulantpresent in the tube by inversion. The blood sample was centrifuged at1500-1800 RCF for 20 min at room temperature (18° C.-25° C.). Plasma wasremoved from the top by aspiration without disturbing the white celllayer containing peripheral mononuclear cells and platelets. Theperipheral mononuclear cells and platelets were carefully removed with aPasteur pipette and collected in a separate tube.

RNA Extraction:

Total RNA was isolated from the isolated peripheral mononuclear bloodcells and platelets using MagNA Pure Compact RNA Isolation Kit (RocheApplied Sciences, Indianapolis, Ind., Catalog number: 04802993001).Briefly, the prefilled cartridges provided in the kit were penetrated bythe disposable piercing tool. Samples are lysed by incubation in lysisbuffer containing chaotropic salt and Proteinase K. RNA was bound to thesurfaces of the added Magnetic Glass Particles and DNA was degraded byincubation with DNase. After several washing steps to remove unboundsubstances, the purified RNA is eluted and was transferred to theElution Tubes. RNA was dissolved in 50 μl of water and is used insubsequent RT/PCR reaction.

cDNA Synthesis:

One (1) to five (5) micrograms of RNA in 13 μl of DEPC-treated water wasadded to a clean microcentrifuge tube. One microliter of either oligo(dT)₁₈ (0.5 μg/μl) or random hexamer solution (50 ng/μ1) was added andmixed gently. The mixture was heated to 70° C. for 10 min, followed byincubation on ice for one minute. The reaction mixture was centrifugedbriefly, followed by the addition of 2 μl of 10× Synthesis buffer (200mM Tris-HCl, pH 8.4, 500 mM KCl, 25 mM Magnesium chloride, 1 mg/ml ofBSA), one μl of 10 mM each of dNTP mix, 2 μl of 0.1 M DTT, one μl ofSuperScript II RT (200 U/μl) (Life Technologies, GIBCO BRL,Gaithersburg, Md.). After gentle mixing, the reaction mixture wassubjected to brief centrifugation, and was incubated at room temperaturefor 10 min. The reaction mixture was further incubated at 42° C. for 50minutes. The reaction was terminated by incubating at 70° C. for 15 min,and then placing it on ice. The reaction mixture is briefly centrifuged,and 1 μl of RNase H (2 Units) was added followed by incubation at 37° C.for 20 min.

Example 2 BCR-ABL Mutation Detection and Analysis

Amplification of the Kinase Domain of BCR-ABL Gene:

The kinase domain of the BCR-ABL gene was amplified by semi-nestedpolymerase chain reaction (PCR) using the cDNA derived from CMLpatient's mRNA as template. Semi-nested PCR was carried out with outerforward, inner forward primer and reverse PCR primers, sequences ofwhich shown below:

Outer forward primer (BCR-F): (SEQ ID NO: 21) TGACCAACTCGTGTGTGAAACTCReverse primer (ABL-R2): (SEQ ID NO: 22) TCCACTTCGTCTGAGATACTGGATTInner forward primer (ABL-F1): (SEQ ID NO: 23) CGCAACAAGCCCACTGTCT

Outer forward primer SEQ ID NO: 21 anneals to BCR exon b2 and thereverse primer SEQ ID NO: 22 anneals to the junction of ABL exon 9 and10. This ensures that un-translocated ABL gene will not be amplified.The second round of PCR (semi-nested PCR) was carried out with using aninner forward primer that anneals to ABL exon 4 (SEQ ID NO: 23) andreverse primer SEQ ID NO: 22. The semi-nested PCR generated a 863 bpamplicon.

The reaction mixture included cDNA (2 μg), 8 μl of 10× synthesis buffer(200 mM Tris-HCl, pH 8.4, 500 mM KCl, 25 mM magnesium chloride, 1 mg/mlof BSA), 68 μl sterile double-distilled water, 1 μl of reverseamplification primer SEQ ID NO: 22 (10 μM), 1 μl of outer of innerforward amplification primers SEQ ID NO: 21 or 23 (10 μM) respectively,1 μl Taq DNA polymerase (2-5 U/μ1) were added. The reaction mixture ismixed gently and the reaction mixture is overlayed with mineral oil. Thereaction mixture is heated to 94° C. for 5 minutes to denature remainingRNA/cDNA hybrids. PCR amplification is then performed in an automatedthermal-cycler for 15-50 cycles, at 94° C. for 1 minute, 55° C. for 30to 90 seconds, and 72° C. for 2 minutes.

Sequencing of PCR Products:

The 863 bp PCR product was extracted from gel, purified was sequencedusing the ABI Prism BigDye® Terminator v3.1 Cycle Sequencing Kit anddetected by ABI PRISM® 3730 Genetic Analyzer (Applied Biosystems, FosterCity, Calif., USA). Sequencing of the PCR product was performed using 2sets of forward and reverse primer pairs. Sequences of the primers areshown below:

(ABL-F1): (SEQ ID NO: 23) CGCAACAAGCCCACTGTCT (ABL-R2): (SEQ ID NO: 22)TCCACTTCGTCTGAGATACTGGATT (ABL-R1): (SEQ ID NO: 24) CAAGTGGTTCTCCCCTACCA(ABL-F2): (SEQ ID NO: 25) TGGTAGGGGAGAACCACTTG

Sequence data was then analyzed by ABI Prism® SeqScape software (AppliedBiosystems, Foster City, Calif., USA) using the ABL sequence (accessionnumber M14752) as a reference. Sequencing indicated four uniquemutations in the BCR-ABL gene: a large deletion of nucleotides2595-2779, a dinucleotide deletion of GA at position 2596-2597, atetranucleotide insertion of CAGG immediately after nucleotide position2417, or a substitution of C to Tat position 2506 of SEQ ID NO: 1.Chromatogram of the sequencing results are shown in FIGS. 2 A-D.Exemplary results of the analysis of the nucleotide sequences of Del2595-2779 mutation by ABI Prism® SeqScape software is shown in FIG. 2 E.

The instant application contains a Sequence Listing which is submittedalong with this application via EFS-Web and is hereby incorporated byreference in its entirety. The ASCII copy, created on Nov. 4, 2009, isnamed 03482707.txt.

Unless otherwise defined, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention belongs. All nucleotide sequencesprovided herein are presented in the 5′ to 3′ direction.

The inventions illustratively described herein may suitably be practicedin the absence of any element or elements, limitation or limitations,not specifically disclosed herein. Thus, for example, the terms“comprising”, “including,” containing”, etc. shall be read expansivelyand without limitation. Additionally, the terms and expressions employedherein have been used as terms of description and not of limitation, andthere is no intention in the use of such terms and expressions ofexcluding any equivalents of the features shown and described orportions thereof, but it is recognized that various modifications arepossible within the scope of the invention claimed.

Thus, it should be understood that although the present invention hasbeen specifically disclosed by preferred examples and optional features,modification, improvement and variation of the inventions embodiedtherein herein disclosed may be resorted to by those skilled in the art,and that such modifications, improvements and variations are consideredto be within the scope of this invention. The materials, methods, andexamples provided here are representative of preferred examples, areexemplary, and are not intended as limitations on the scope of theinvention.

The invention has been described broadly and generically herein. Each ofthe narrower species and subgeneric groupings falling within the genericdisclosure also form part of the invention. This includes the genericdescription of the invention with a proviso or negative limitationremoving any subject matter from the genus, regardless of whether or notthe excised material is specifically recited herein.

In addition, where features or aspects of the invention are described interms of Markush groups, those skilled in the art will recognize thatthe invention is also thereby described in terms of any individualmember or subgroup of members of the Markush group.

All publications, patent applications, patents, and other referencesmentioned herein are expressly incorporated by reference in theirentirety, to the same extent as if each were incorporated by referenceindividually. In case of conflict, the present specification, includingdefinitions, will control.

Other examples are set forth within the following claims.

What is claimed is:
 1. A method for determining the prognosis of apatient diagnosed as having a myeloproliferative disease comprising: (a)assaying a nucleic acid sample comprising a BCR-ABL nucleic acidobtained from the patient to determine the presence of one or moreBCR-ABL truncation mutations selected from the group consisting of2417insCAGG, Del 2596-2597, and C2506T, wherein assaying comprises: (i)performing a nucleic acid amplification reaction on the BCR-ABL nucleicacid sample with at least one primer pair comprising a forward primerthat binds to ABL exon 4 and a reverse primer that binds to the junctionof ABL exon 9 and exon 10; (ii) contacting the amplified BCR-ABL nucleicacid with a detectably labeled nucleic acid probe that specificallyhybridizes to a mutant BCR-ABL nucleic acid comprising the mutation, ifpresent, but not to a wild-type BCR-ABL nucleic acid comprising SEQ IDNO: 1, wherein: (1) the detectably labeled nucleic acid probe fordetecting the 2417insCAGG mutation comprises at least 20 contiguousnucleotides of SEQ ID NO: 13; (2) the detectably labeled nucleic acidprobe for detecting the Del 2596-2597 mutation comprises at least 20contiguous nucleotides of SEQ ID NO: 8; and (3) the detectably labelednucleic acid probe for detecting the C2506T mutation comprises at least20 contiguous nucleotides of SEQ ID NO: 18; and (iii) detecting theBCR-ABL truncation mutation when a hybrid is formed between thedetectably labeled nucleic acid probe and the BCR-ABL nucleic acid; and(b) identifying said patient as having poor prognosis when said one ormore mutations are present.
 2. The method of claim 1, wherein saidmyeloproliferative disease is CML.
 3. The method of claim 1, whereinsaid myeloproliferative disease is ALL.
 4. A method for predicting thelikelihood for resistance to treatment with a tyrosine kinase inhibitorin a patient diagnosed as having a myeloproliferative disease,comprising: (a) assaying a nucleic acid sample comprising a BCR-ABLnucleic acid obtained from the patient to determine the presence of oneor more BCR-ABL truncation mutations selected from the group consistingof 2417insCAGG, Del 2596-2597, and C2506T, wherein assaying comprises:(i) performing a nucleic acid amplification reaction on the BCR-ABLnucleic acid sample with at least one primer pair comprising a forwardprimer that binds to ABL exon 4 and a reverse primer that binds to thejunction of ABL exon 9 and exon 10; (ii) contacting the amplifiedBCR-ABL nucleic acid with a detectably labeled nucleic acid probe thatspecifically hybridizes to a mutant BCR-ABL nucleic acid comprising themutation, if present, but not to a wild-type BCR-ABL nucleic acidcomprising SEQ ID NO: 1, wherein: (1) the detectably labeled nucleicacid probe for detecting the 2417insCAGG mutation comprises at least 20contiguous nucleotides of SEQ ID NO: 13; (2) the detectably labelednucleic acid probe for detecting the Del 2596-2597 mutation comprises atleast 20 contiguous nucleotides of SEQ ID NO: 8; and (3) the detectablylabeled nucleic acid probe for detecting the C2506T mutation comprisesat least 20 contiguous nucleotides of SEQ ID NO: 18; and (iii) detectingthe BCR-ABL truncation mutation when a hybrid is formed between thedetectably labeled nucleic acid probe and the BCR-ABL nucleic acid; and(b) identifying said patient as having a likelihood of resistance to atyrosine kinase inhibitor when one or more said mutations are present.5. The method of claim 4, wherein said tyrosine kinase inhibitor is oneor more selected from the group consisting of imatinib, nilotinib anddasatinib.
 6. The method of claim 4, wherein said tyrosine kinaseinhibitor is imatinib.
 7. The method of claim 4, wherein saidmyeloproliferative disease is CML.
 8. The method of claim 4, whereinsaid myeloproliferative disease is ALL.
 9. The method of claim 4,wherein said patient is being administered a tyrosine kinase inhibitor.10. The method of claim 9, wherein said tyrosine kinase inhibitor is oneor more selected from the group consisting of imatinib, nilotinib anddasatinib.
 11. The method of claim 10, wherein the treatment regimen ofthe patient is modified when at least one of said mutations isidentified.
 12. The method of claim 1, wherein the treatment regimen ofthe patient is modified when at least one of said mutations isidentified.
 13. The method of claim 1, wherein nucleic acidamplification comprises real-time polymerase chain reaction (RT-PCR).14. The method of claim 4, wherein nucleic acid amplification comprisesreal-time polymerase chain reaction (RT-PCR).
 15. A method for detectingone or more BCR-ABL truncation mutations selected from the groupconsisting of 2417insCAGG, Del 2596-2597, and C2506T, comprising: (a)contacting a nucleic acid sample comprising a BCR-ABL nucleic acid froma human patient or a BCR-ABL nucleic acid isolated therefrom with adetectably labeled nucleic acid probe that specifically hybridizes to amutant BCR-ABL nucleic acid comprising the mutation, if present, but notto a wild-type BCR-ABL nucleic acid comprising SEQ ID NO: 1, wherein:(i) performing a nucleic acid amplification reaction on the BCR-ABLnucleic acid sample with at least one primer pair comprising a forwardprimer that binds to ABL exon 4 and a reverse primer that binds to thejunction of ABL exon 9 and exon 10; (ii) the detectably labeled nucleicacid probe for detecting the 2417insCAGG mutation comprises at least 20contiguous nucleotides of SEQ ID NO: 13; (iii) the detectably labelednucleic acid probe for detecting the Del 2596-2597 mutation comprises atleast 20 contiguous nucleotides of SEQ ID NO: 8; and (iv) the detectablylabeled nucleic acid probe for detecting the C2506T mutation comprisesat least 20 contiguous nucleotides of SEQ ID NO: 18; and (b) detectingthe BCR-ABL truncation mutation when a hybrid is formed between thedetectably labeled nucleic acid probe and the BCR-ABL nucleic acid. 16.The method of claim 15, wherein nucleic acid amplification comprisesreal-time polymerase chain reaction (RT-PCR).
 17. The method of claim15, wherein the nucleic acid sample is obtained from a patient diagnosedas having a myeloproliferative disease.
 18. The method of claim 17,wherein said myeloproliferative disease is CIVIL or ALL.
 19. The methodof claim 17, wherein said patient is being administered a tyrosinekinase inhibitor.
 20. The method of claim 19, wherein said tyrosinekinase inhibitor is one or more imatinib, nilotinib and dasatinib. 21.The method of claim 1, wherein the forward primer comprises SEQ ID NO:23.
 22. The method of claim 1, wherein the reverse primer comprises SEQID NO:
 22. 23. The method of claim 4, wherein the forward primercomprises SEQ ID NO:
 23. 24. The method of claim 4, wherein the reverseprimer comprises SEQ ID NO:
 22. 25. The method of claim 15, wherein theforward primer comprises SEQ ID NO:
 23. 26. The method of claim 15,wherein the reverse primer comprises SEQ ID NO: 22.